RELATED APPLICATIONS This application claims the benefit of U.S. Provisional Applications No. 63/265,994 filed on Dec. 23, 2021, and 63/334,634 filed on Apr. 25, 2022. The entire teachings of the above applications are incorporated herein by reference.
GOVERNMENT SUPPORT This invention was made with government support under GM046779 and GM135087 from National Institutes of Health. The government has certain rights in the invention.
INCORPORATION BY REFERENCE OF MATERIAL IN ASCII TEXT FILE This application incorporates by reference the Sequence Listing contained in the following eXtensible Markup Language (XML) file being submitted concurrently herewith:
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BACKGROUND Fragile X Syndrome (FXS) lies on the autism spectrum and is the most frequent inherited form of intellectual impairment. FXS afflicts 1 in 4000 boys and 1 in 7000 girls. In addition to intellectual impairment, children with FXS present a range of symptoms, including speech and developmental delays, perseveration, hyperactivity, aggression, and epilepsy, among other maladies. FXS is caused by a CGG triplet repeat expansion in a single gene, FMR1, which resides on the X chromosome. When the CGG triplet expands to 200 or more, the FMR1 gene is methylated and thereby transcriptionally inactivated. The loss of the FMR1 gene product, the protein fragile X messenger ribonucleotide protein (FMRP), is the cause of the disorder.
SUMMARY In one aspect, the present disclosure provides a method of diagnosing a subject as having, or having a propensity to develop, a fragile X-associated disorder, the method comprises assaying at least one biomarker in a biological sample (e.g., a non-neural biological sample) from the subject, wherein the level and/or splicing of the at least one biomarker in the biological sample is indicative of the subject as having, or having a propensity to develop, a fragile X-associated disorder.
In another aspect, the present disclosure provides a method of prognosing a fragile X-associated disorder in a subject, comprising assaying at least one biomarker in a biological sample (e.g., a non-neural biological sample) from the subject, wherein the level and/or splicing of the at least one biomarker in the biological sample is indicative of the subject as having a propensity to have a poorer prognosis of the fragile X-associated disorder.
In another aspect, the present disclosure provides a method of predicting a treatment outcome of a fragile X-associated disorder in a subject, comprising assaying at least one biomarker in a biological sample (e.g., a non-neural biological sample) from the subject, wherein the level and/or splicing of the at least one biomarker in the biological sample is indicative of the subject as having a propensity to have a poorer treatment outcome.
In certain embodiments, the at least one biomarker is a RNA biomarker.
In some embodiments, the fragile X-associated disorder is FXS.
In some embodiments, the biological sample is a non-brain tissue sample. In certain embodiments, the biological sample is a non-neural biological sample, i.e., a sample that does not comprise any neurons.
In some embodiments, the at least one RNA biomarker is selected from the group consisting of AGAP1, RAB25, FAM3B, XKR3, MAP3K15, LEP, RP11-706O15.3, GCOM1, CXCL6, RGL3, NECAB2, TGM3, LRRC6, MAB21L3, RP11-36B15.1, AC091878.1, RP11-154H23.3, NOV, AC093495.4, RP11-455F5.6, RGPD2, COL9A3, CLEC18A, RP11-256L6.2, LINC01127, SLC38A11, EFCAB12, LA16c-380H5.5, CXCL1, RP11-1334A24.5, AC100793.2, ANKDD1A, AVIL, RP11-44F14.8, RP11-290F20.1, AC116366.5, EPHB4, ST6GALNAC3, PANX2, CREB5, KIAA0319, HECW2, ADCY4, LINC00173, RP11-59D5_B.2, RP11-274B18.2, RP11-213H15.3, CORO7-PAM16, HAL, DPEP3, AC002467.7, MGAM, PNMA8A, FMR1, S100B, RP11-885N19.6, RP11-545I5.3, AC091814.2, KLRC2, L1TD1, PGBD5, MXRA7, CROCC2, SEMA5A, PLA2G4C, RP11-1008C21.1, TANC1, C4orf50, NUAK1, AC104809.4, RGS17, KCNS1, DRAXIN, B3GAT1, ARHGEF28, KIF19, APOL4, GZMH, GAS1, SCD5, GLB1L2, IGHA1, KNVDC1, RP11-383H13.1, FGFR2, TFCP2L1, PDGFRB, LAG3, GPR153, PODN, CKB, CERCAM, ZNF365, JUP, TRNP1, JAKMIP1, CPXM1, SLC1A7, LGR6, FCRL6, MORN4, TUBB2A, PRSS23, BFSP1, NCALD, ZNF573, PAK1, MIR4435-2HG, CD8B, PDGFC, TRAPPC2L, AC006504.5, ZNF512, FAM228B, NEIL2, FAM78A, FYB1, RNF216P1, ZCWPW1, DTX2, ATP5MD, MX2, LYRM1, GUF1, DPH7, NSFL1C, MTMR1, GTPBP10, RGS3, DRAM2, RHOH, LAIR2, GBP3, GTF2H1, XPNPEP3, ZNF888, TBC1D5, AC060780.1, SDHAP2, KMT2A, SH3BP2, CSNK1G2, NSUN5P1, LINC01128, RNF19A, SNHG8, TOP1MT, AL135818.1, CR1, CRIM1, NAP1L1, AC004593.2, SEC61A2, PCNX2, TPT1-AS1, HLA-A, LUCAT1, PTPN2, SEC31B, POLR2J3, POLR2J4, CAST, POLR2J4, NUMBL, PRMT7, ATF7IP2, TIMM23B-AGAP6, ADGRE2, GTF2H2B, MICA, SLC29A2, ZBTB10, NLGN3, METTL25, ADAM15, SSH1, SIRPB1, PARP2, PACRGL, ENTPD1-AS1, FUZ, SDR39U1, EPOR, ZSCAN26, SNHG17, GPS2, NECAP1, MRPL11, DNAJC19, ANKZF1, C1orf162, PIGT, SLC25A37, AP1G1, CIC, ITGB7, ATG16L2, BECN1, ARHGEF40, BANP, PIGA, RAD52, IRF3, CEP78, SPINT1, TMEM156, NT5C3B, PLD2, ANKRD12, CASP8, PACS2, HLA-DMA, DHPS, PDCD6, SNX5, MPPE1, AC016394.2, DPM1, E2F5, PTPN7, MTFP1, TOR1AIP1, POT1, JOSD2, NLRX1, FDXR, ZDHHC16, ALKBH4, RPS9, ZNF302, TENT4B, TKT, CARD8, RBM26, WSB1, DDX60L, ATP11A, SRGAP2, CEACAM21, COX18, WDR47, PATZ1, POLM, CC2D1B, CLK4, MIB2, PHF1, KANSL1, TCF3, and combinations thereof.
In another aspect, the present disclosure provides a method of stratifying a population of subjects having, or having a propensity to develop, a fragile X-associated disorder (e.g., FXS), comprising assaying non-neural biological samples from the subjects for the presence of FMR1 RNA isoform 12.
In another aspect, the present disclosure provides a method for assessing the efficacy of a drug for treatment of a fragile X-associated disorder (e.g., FXS), comprising stratifying a population of subjects to create a stratified population comprising a subpopulation who has the FMR1 RNA isoform 12 and a subpopulation who does not have the FMR1 RNA isoform 12, and administering the drug to the subpopulation who has FMR1 RNA isoform 12, or to both subpopulations.
In another aspect, the present disclosure provides a method of stratifying a set of subjects having a fragile X-associated disorder (e.g., FXS), comprising assaying FMR1 RNA in a biological sample from the subject, and stratifying the set of subjects for treatment based on the presence and/or level of the FMR1 RNA isoform 12 in the biological sample.
BRIEF DESCRIPTION OF THE DRAWINGS The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawings will be provided by the Office upon request and payment of the necessary fee.
The foregoing will be apparent from the following more particular description of example embodiments, as illustrated in the accompanying drawings in which like reference characters refer to the same parts throughout the different views. The drawings are not necessarily to scale, emphasis instead being placed upon illustrating embodiments.
FIG. 1 is a volcano plot of log 2FC of RNA levels (FXS vs typically developing (TD)). Statistically significant changes (P value<0.0002) are shown as black dots (down-regulated) and white dots (up-regulated). Gray dots refer to unchanged RNAs.
FIG. 2 is a heat map for RNA clustering based on z-scores of differentially expressed genes in leukocytes from FXS (N=29) vs TD (N=13) individuals.
FIG. 3 shows histograms for transcripts per million (TPM) values for RNAs that are up or down-regulated in FXS vs TD. *p<0.05; **p<0.01).
FIG. 4 shows histograms of RT-qPCR validations of up or down-regulated RNAs in FXS (N=7) and TD (N=5) leukocytes.
FIG. 5 shows histograms of RT-qPCR analysis of S100B, RAB25, and GAPDH RNAs in FXS2 LCLs compared to TD1 LCLS. The amounts of S100B and RAB25 were made relative to GAPDH. (*P<0.05, **P<0.01, t test).
FIG. 6A shows a summary table for changes in alternative splicing events in FXS vs TD leukocytes detected by rMATS at an FDR<5% and a difference in the exon inclusion levels (PSI, Percent spliced-in) between the genotypes (deltaPSI) of ≥5%. Schematic for the splicing event categories is shown at the left of the table. FIG. 6B shows violin plots of alternative splicing in FXS vs TD leukocytes indicating PSI for each type event.
FIG. 7A shows inclusion levels for exon 3 of LAIR2 RNA in FXS vs TD samples from rMATS analysis. FIG. 7B shows RT-PCR exon 3 skipping of the LAIR2 RNA in TD (N=3) and FXS (N=9) samples.
FIG. 8 is a volcano plot showing statistically significant changes (Padj<0.05) of RNA markers with increased (428, “x”) or reduced (305, “Δ”) expression levels in the white blood cells (WBCs) of fragile X syndrome (FXS) individuals (patients) versus WBCs from typically developing (TD) individuals. Gray dots refer to unchanged RNAs.
FIG. 9 is a heat map for RNA clustering based on z-scores of differentially expressed genes in leukocytes from FXS (N=7) vs TD (N=10) individuals.
FIG. 10 shows metagene profiles using deepTools 2 for distribution of H3K4me3 marks along gene lengths. A similar increase in ChIP signal irrespective of genotype was seen at the transcription start site (TSS) for the H3K4me3 ChIP.
FIG. 11 shows metagene profiles using deepTools 2 for distribution of H3K36me3 marks along gene lengths. A similar increase in ChIP signal irrespective of genotype was seen in the gene body and transcription end site (TES) for H3K36me3 ChIP.
FIG. 12 shows changes in the alternative polyadenylation site (Ln-long 3′UTR-distal polyA site usage, Sh-Short 3′UTR-proximal polyA site usage) between the genotypes (P<0.05, average reads count>5 in each replicate in each region (aUTR and cUTR)).
FIG. 13 shows changes in intronic polyadenylation (IPA) site usage between the genotypes (P<0.05, average reads count>5 in each replicate in each region (aUTR and cUTR)).
FIG. 14 shows a genome browser view of PNMA8A RNA, showing exons and introns. PNMA8A RNA was strongly expressed in the white blood cells of FXS individuals and virtually absent in the white blood cells of typically developing individuals.
FIG. 15 shows a genome browser view of XKR3 RNA, showing exons and introns. XKR3 RNA was strongly expressed in the white blood cells of FXS individuals and virtually absent in the white blood cells of typically developing individuals.
FIG. 16 shows a genome browser view of S100B, showing exons and introns. S100B RNA expression was reduced in the white blood cells of FXS individuals, compared to typically developing individuals.
FIG. 17 is a scatter plot of percent spliced in (PSI) of skipped exons (SE) in white blood cells of FXS individuals versus typically developing individuals. The symbol “x” represents RNA markers having an increased exon skipping in FXS individuals relative to typically developing individuals. The symbol “▴” represents RNA markers having a reduced exon skipping in FXS individuals relative to typically developing individuals. All data are statistically significant (p<0.05 and FDR<0.05). NC: No change in alternative exons in 17064 RNAs, AS UP: Increased alternative exon inclusion in 419 RNAs, AS DOWN: Decreased alternative exon inclusion in 705 RNAs.
FIG. 18 is a scatter plot of percent spliced in (PSI) of mutually excluded exons (MXE) in white blood cells of FXS individuals versus typically developing individuals. 689 RNA markers had a decreased mutually exclusive exon switching in FXS individuals relative to typically developing individuals (“x”, less inclusion of mutually excluded exon) and 571 RNA markers had an increased mutually exclusive exon switching in FXS individuals relative to typically developing individuals (“▴”, more inclusion of mutually excluded exon). All data are statistically significant (p<0.05 and FDR<0.05).
FIG. 19 shows gene ontology terms for biological processes using clusterProfiler (v3.12.0) (Yu et al., 2012) enriched in RNAs up-regulated (top) and down-regulated (bottom) in FXS leukocytes relative to TD (Padj value<0.05).
FIG. 20 summarizes changes in alternative splicing events in FXS vs TD leukocytes detected by rMATS (Shen et al., 2014) at an FDR<5% and a difference in the exon inclusion levels (PSI, Percent spliced-in) between the genotypes (deltaPSI) of ≥5% and read counts >1 in each sample. Schematic for the splicing event categories is shown at the left of the table.
FIG. 21 shows normalized gene counts (transcripts per million, TPM) obtained from RNA-seq data analysis for total FMR1 (all isoforms), FMR1-205 (encodes full-length 632 amino acid FMRP), FMR1-217 (a mis-spliced RNA), and FXR2, a paralogue of FMR1. The scale from light grey to dark gray denotes highest to lowest gene counts.
FIG. 22 shows a genome browser view of RNA-seq data for FXS and TD individuals for the FMR1 gene. FMR1 RNA is detected in all TD individuals (top 13 reads) and FXS individuals 1-21 show (bottom 29 reads). The black box marked on the FMR1 gene illustrated at the bottom shows the region of intron 1 with differential reads between TD (1-13) and FXS (1-21) individuals.
FIG. 23 shows an expanded view of FMR1 exon 1 and intron 1. The reads displayed here map to an exon that comprises the annotated FMR1-217 isoform. All annotated FMR1 isoforms and sequence data for FMR1-217 PCR fragments from FXS RNA sample are shown in FIG. 24. H refers to high and L refers to low FMR1.
FIG. 24 shows FMR1 isoforms annotated in the GRCh38.p13 genome assembly. The FMR1-217 isoform (ENST00000621447.1) is marked with a grey box.
FIG. 25 shows changes in intronic polyadenylation (IPA) site usage between the genotypes (P<0.05, average reads count>5 in each replicate in each region (aUTR and cUTR)).
FIG. 26 shows the full length FMR1 RNA and the FMR1-217 isoform illustrated with the CGG repeats in the 5′ UTR. The proportion of full length FMR1 to FMR1-217 was quantified by RT-qPCR in TD, H FMR1 and L FMR1 individuals. The forward (F) and reverse (R) primers used for q-PCR are shown. The total FMR1 RNA relative to GAPDH RNA levels was significantly reduced in H FMR1 and L FMR1 vs TD (* represents P<0.05, t test). Bar graphs indicate mean, Error bars indicate+/−SEM.
FIG. 27 is a volcano plot of log 2FC of RNA level changes (L FMR1 vs H FMR1). Statistically significant changes (Padj value<0.05) are enlarged black dots circled by a thick line (down-regulated) and enlarged black dots left un-circled (up-regulated) relative to unchanged RNAs (smaller light gray dots).
FIGS. 28A-28B are scatter plots of percent spliced in (PSI) of skipped exon (SE) or mutually excluded exon (MXE) in the white blood cells of FXS individuals who expressed FMR1 RNA isoform 12 versus those who did not. FIG. 29A. The symbol “x” represents RNA markers having an increased exon skipping in isoform 12-expressing FXS individuals relative to those who did not. The symbol “▴” represents RNA markers having a reduced exon skipping in isoform 12-expressing FXS individuals relative to those who did not. FIG. 29B. The symbol “x” represents RNA markers having a reduced mutually exclusive exon switching in isoform 12-expressing FXS individuals relative to those who do not. The symbol “▴” represents RNA markers having an increased mutually exclusive exon switching in isoform 12-expressing FXS individuals relative to those who did not.
FIG. 29 is a summary table of changes in alternative splicing events from L FMR1 vs H FMR1 samples detected by rMATS (Shen et al., 2014) at an FDR<5% and a difference in the exon inclusion levels (PSI, Percent spliced-in) between the genotypes (deltaPSI) of ≥5%. Read counts >1 in each sample are depicted. Schematic for the splicing event categories is shown at the left of the table.
FIG. 30 shows changes in the alternative polyadenylation site (Ln-long 3′UTR-distal polyA site usage, Sh-Short 3′UTR-proximal polyA site usage) between the genotypes (P<0.05, average reads count>5 in each replicate in each region (aUTR and cUTR)).
FIG. 31 depicts sample information for postmortem FXS frontal cortex and premutation FXS carriers and TD individuals (derived from (Tran et al., 2019)). RNA-seq datasets GSE107867 (NIH samples) and GSE117776 were reanalyzed for DGE, DAS and APA. The TPM for FMR1 RNA in the samples is shown.
FIG. 32A shows Integrative Genomics Viewer (IGV) tracks of RNA-seq data (Tran et al., Widespread RNA editing dysregulation in brains from autistic individuals, Nat. Neurosci. (2019)) for FXS and TD individuals for the FMR1 gene. FIG. 32B IGV tracks of selected regions of FMR1 re-analyzed from the RNA-seq data of Vershkov et al., FMR1 Reactivating Treatments in Fragile X iPSC-Derived Neural Progenitors In Vitro and In Vivo, Cell Rep. 26: 2531-39 (2019), who deleted the FMR1 CGG expansion by CRISPR/Cas9 gene editing. Biologic duplicate of iPSC-derived neural stem cells (NSCs) from FXS individuals (FXS-NSC) treated with vehicle or 5-aza-2-deoxycytidine (5-azadC) as well as isogenic CGG-edited samples are shown. FMR1-217 reads are detected only in the 5-azadC-treated samples. FIG. 32C IGV tracks of selected regions of FMR1 re-analyzed from the RNA-seq data of Liu et al. Rescue of Fragile X Syndrome Neurons by DNA Methylation Editing of the FMR1 Gene, Cell 172: 979-91 (2018), who performed targeted FMR1 gene demethylation in FXS iPSCs and iPSC-derived neurons. iPSCs derived from FXS individuals were incubated with viruses expressing a mock guide RNA (i_mock), or an FMR1 guide RNA and catalytically inactive Cas9 fused to the Tet1 demethylase (i_Tet1). iPSC-derived neurons from to FXS individuals were treated with a mock guide RNA (N1_mock, N2_mock), or an FMR1 guide RNA and catalytically inactive Cas9 fused to the Tet1 demethylase (N1_Tet1, N2_Tet1, N3_Tet1). All cells were incubated with an FMR1 guide RNA and catalytically inactive Cas9 fused to the Tet1 demethylase express FMR1-217.
FIG. 33 is a volcano plot of log 2FC of RNA level changes (FXS vs TD (UCD), N=2/genotype). Statistically significant changes (Padj value<0.05) are shown in enlarged black dots circled by a thick line (down-regulated) and enlarged black dots left un-circled (up-regulated) relative to unchanged RNAs (smaller light gray dots).
FIG. 34 is a summary table of changes in alternative splicing events FXS vs TD (Univ of California at Davis) and FXS vs FXS carriers (NIH NeuroBioBank) detected by rMATS (Shen et al., 2014) at an FDR<5% and a difference in the exon inclusion levels (PSI, Percent spliced-in) between the genotypes (deltaPSI) at ≥5%. Read counts >1 in each sample are depicted. Schematic for the splicing event categories is shown at the left of the table.
FIG. 35 depicts the experimental design for RNA extraction from post-mortem cortical tissue obtained from 6 FXS males (F1-F6) and 5 typically developing (T1-T5) age-matched males. RT-qPCR data for cortical tissue-derived RNA samples representing abundance for FMR1 and FMR1-217 isoforms relative to GAPDH RNA. Each sample was analyzed in duplicate. Primers used for amplification are represented in FIG. 26 (P<0.01**, t test).
FIG. 36 depicts a schematic diagram of fibroblast generated from skin biopsies obtained from three male premutation carriers (P1-P3) and three male TD individuals (T1-T3). The table shows patient de-identified designation, genotypes, and CGG repeat numbers in the 5′UTR in the FMR1 gene. ND, not determined. qPCR data for fibroblast-derived RNA samples representing abundance for FMR1 and FMR1-217 isoforms relative to GAPDH RNA. Each sample was analyzed in duplicate. Primers used for amplification are represented in FIG. 26.
FIG. 37 shows sample information for lymphoblast cell lines (LCLs) (Coriell Institute, NJ) from two FXS and two TD members of a family are shown. FMRP and GAPDH (loading control) levels were determined by western blots. Ratios of FMRP/GAPDH normalized to FXS1 are shown below the blot.
FIG. 38 shows the proportion of full length FMR1 to FMR1-217 quantified using RT-qPCR in the TD and FXS2 LCLs relative to GAPDH RNA levels. Primers used for q-PCR are shown in the gene illustration. The total FMR1 RNA was unchanged but the proportion of FMR1-217 was significantly higher in FXS2 LCL compared to TD LCL.
FIG. 39 shows the proportion of full length FMR1 to FMR1-217 quantified using RT-qPCR in the FXS1 and FXS2 LCLs treated with 5-AzadC relative to vehicle, normalized to GAPDH RNA levels (** represents P<0.001, t test). FMRP levels were determined using western blots relative to GAPDH in FXS1 and FXS2 LCLs treated with DMSO or 5-AzadC. Ratios of FMRP/GAPDH are shown below the blots. Histograms indicate mean values; error bars indicate+/−SEM.
FIG. 40 shows changes in the alternative polyadenylation site (Ln-long 3′UTR-distal poly(A) site usage, Sh-Short 3′UTR-proximal poly(A) site usage) between the genotypes (P<0.05, average reads count>5 in each replicate in each region (aUTR and cUTR))
FIG. 41 is a volcano plot of log 2FC of RNA level change (FXS vs pre-mutation carriers (NIH), N=2/genotype). Statistically significant changes (Padj value<0.05) are shown in enlarged black dots circled by a thick line (down-regulated), and enlarged black dots left un-circled (up-regulated) relative to unchanged RNAs (smaller light gray dots).
FIG. 42 shows changes in the alternative polyadenylation site (Ln-long 3′UTR-distal poly(A) site usage, Sh-Short 3′UTR-proximal poly(A) site usage) between the genotypes (P<0.05, average reads count>5 in each replicate in each region (aUTR and cUTR)).
FIG. 43 shows a summary of statistically significant RNA events distinguishing FXS individuals from typically developing individuals, and FXS individuals who express FMR1 RNA isoform 12 from those who did not.
FIG. 44 shows correlation of FXS molecular parameters with IQ. Three-dimensional comparison of indicated parameters. The inset shows samples with 100% methylation. The increasing size of the dots represent increase in FMRP levels, and the darkness from low to high represent increase in IQ levels.
DETAILED DESCRIPTION A description of example embodiments follows.
Several aspects of the invention are described below, with reference to examples for illustrative purposes only. It should be understood that numerous specific details, relationships, and methods are set forth to provide a full understanding of the invention. One having ordinary skill in the relevant art, however, will readily recognize that the invention can be practiced without one or more of the specific details or practiced with other methods, protocols, reagents, cell lines and animals. The present invention is not limited by the illustrated ordering of acts or events, as some acts may occur in different orders and/or concurrently with other acts or events. Furthermore, not all illustrated acts, steps or events are required to implement a methodology in accordance with the present invention. Many of the techniques and procedures described, or referenced herein, are well understood and commonly employed using conventional methodology by those skilled in the art.
Unless otherwise defined, all terms of art, notations and other scientific terms or terminology used herein are intended to have the meanings commonly understood by those of skill in the art to which this invention pertains. In some cases, terms with commonly understood meanings are defined herein for clarity and/or for ready reference, and the inclusion of such definitions herein should not necessarily be construed to represent a substantial difference over what is generally understood in the art. It will be further understood that terms, such as those defined in commonly-used dictionaries, should be interpreted as having a meaning that is consistent with their meaning in the context of the relevant art and/or as otherwise defined herein.
The terminology used herein is for the purpose of describing particular embodiments only and is not intended to be limiting.
As used herein, the indefinite articles “a,” “an” and “the” should be understood to include plural reference unless the context clearly indicates otherwise.
Throughout this specification and the claims which follow, unless the context requires otherwise, the word “comprise,” and variations such as “comprises” and “comprising”, will be understood to imply the inclusion of, e.g., a stated integer or step or group of integers or steps, but not the exclusion of any other integer or step or group of integer or step. When used herein, the term “comprising” can be substituted with the term “containing” or “including.”
“About” means within an acceptable error range for the particular value, as determined by one of ordinary skill in the art. Typically, an acceptable error range for a particular value depends, at least in part, on how the value is measured or determined, e.g., the limitations of the measurement system. For example, “about” can mean within an acceptable standard deviation, per the practice in the art. Alternatively, “about” can mean a range of ±20%, e.g., ±10%, ±5% or ±1% of a given value. It is to be understood that the term “about” can precede any particular value specified herein, except for particular values used in the Exemplification. When “about” precedes a range, as in “about 24-96 hours,” the term “about” should be read as applying to both of the given values of the range, such that “about 24-96 hours” means about 24 hours to about 96 hours.
As used herein, “consisting of” excludes any element, step, or ingredient not specified in the claim element. When used herein, “consisting essentially of” does not exclude materials or steps that do not materially affect the basic and novel characteristics of the claim. Any of the terms “comprising,” “containing,” “including,” and “having,” whenever used herein in the context of an aspect or embodiment of the invention, can in some embodiments, be replaced with the term “consisting of,” or “consisting essentially of” to vary scopes of the disclosure.
As used herein, the conjunctive term “and/or” between multiple recited elements is understood as encompassing both individual and combined options. For instance, where two elements are conjoined by “and/or,” a first option refers to the applicability of the first element without the second. A second option refers to the applicability of the second element without the first. A third option refers to the applicability of the first and second elements together. Any one of these options is understood to fall within the meaning, and, therefore, satisfy the requirement of the term “and/or” as used herein. Concurrent applicability of more than one of the options is also understood to fall within the meaning, and, therefore, satisfy the requirement of the term “and/or.”
When a list is presented, unless stated otherwise, it is to be understood that each individual element of that list, and every combination of that list, is a separate embodiment. For example, a list of embodiments presented as “A, B, or C” is to be interpreted as including the embodiments, “A,” “B,” “C,” “A or B,” “A or C,” “B or C,” or “A, B, or C.”
When introducing elements disclosed herein, the articles “a,” “an,” “the,” and “said” are intended to mean that there are one or more of the elements. Further, the one or more elements may be the same or different. Thus, for example, unless the context clearly indicates otherwise, “a biomarker” includes a single biomarker, and two or more biomarkers. Further the two or more biomarkers can be the same or different as, for example, in embodiments wherein a first biomarker has a reduced expression and a second biomarker has an increased alternative 5′ splicing.
The term “poor” or “poorer” refers to greater degree of fragile X-associated disorder (e.g., FXS) symptoms, increased extent of disease, decreased (i.e., worsening) state of disease, increased or enhanced state of disease progression, deterioration or worsening of the disease state, whether detectable or undetectable.
Methods and Compositions for Diagnosing/Prognosing Fragile X-Associated Disorders In one aspect, the present disclosure provides a method of diagnosing a subject as having, or having a propensity to develop, a fragile X-associated disorder, the method comprising assaying at least one biomarker (e.g., RNA biomarker) in a biological sample from the subject, wherein the level and/or splicing of the at least one RNA biomarker in the biological sample is indicative of the subject as having, or having a propensity to develop, a fragile X-associated disorder.
In another aspect, the present disclosure provides a method of prognosing a fragile X-associated disorder in a subject, comprising assaying at least one biomarker (e.g., RNA biomarker) in a biological sample from the subject, wherein the level and/or splicing of the at least one RNA biomarker in the biological sample is indicative of the subject as having a propensity to have a poorer prognosis of the fragile X-associated disorder.
In another aspect, the present disclosure provides a method of predicting a treatment outcome of a fragile X-associated disorder in a subject, comprising assaying at least one biomarker (e.g., RNA biomarker) in a biological sample from the subject, wherein the level and/or splicing of the at least one RNA biomarker in the biological sample is indicative of the subject as having a propensity to have a poorer treatment outcome.
Fragile X-Associated Disorders Fragile X-associated disorders are caused by mutation of the fragile X messenger ribonucleoprotein 1 (FMR1, previously known as fragile X mental retardation 1) gene, located in the q27.3 loci of the X chromosome. The expansion of the trinucleotide CGG above the normal range (greater than 54 repeats) in the non-coding region of the FMR1 gene has been associated with the development of the fragile X-associated disorders in those carrying the premutation (55-200 CGG repeats). Non-limiting examples of fragile X-associated disorders include fragile-X associated tremor/ataxia syndrome (FXTAS), fragile X-associated primary ovarian insufficiency (FXPOI), fragile X-associated neuropsychiatric disorders (FXAND), and fragile X syndrome (FXS). In some embodiments, the fragile X-associated disorder is FXS.
Biological Samples As used herein, “biological sample” refers to any sample that can be from or derived from a human subject. The methods disclosed herein can be performed using RNA molecules obtained from a variety of possible biological sample types. For example, a single cell or cell lysate, a population of cells, a cell culture, a tissue, or a biological fluid.
In some embodiments, the biological sample is a non-brain sample. In certain embodiments, the biological sample is a non-neural biological sample. In some embodiments, the biological sample is a bodily fluid sample, a hair sample (e.g., from hair follicles), nasal (e.g., nasal swab) sample, buccal (e.g., buccal swab) sample or a skin sample. Non-limiting examples of biological fluids (bodily fluids) include blood (e.g., whole blood and derivatives and fractions of blood, such as plasma or serum), bone marrow aspirates, cerebrospinal fluid, extracted galls, GCF gingival crevicular fluid, milk, prostate fluid, pus, saliva (including whole saliva, individual gland secretions, oral rinse), skin scrapes, sputum, surface washings, tears (liquid secreted by lacrimal glands), and urine. In certain embodiments, the bodily fluid comprises blood, saliva, sputum, tears, urine or semen, or a combination thereof. In particular embodiments, the bodily fluid comprises white blood cells.
In other embodiments, the biological sample is a brain sample.
In certain embodiments, the biological sample comprises a fetal cell (e.g., circulating fetal cell), a blastomere, a trophectoderm cell, a stem cell (e.g., induced pluripotent stem cell (iPSC) or derived stem cell), a fibroblast (e.g., a dermal derived fibroblast cell or lung-derived fibroblast cell), a modified fibroblast, a leukocyte, a pluripotent cell, or a cultured cell.
Biomarkers As used herein, “biomarker” refers to a nucleotide sequence (e.g., RNA) or encoded product thereof (e.g., a protein) used as a point of reference when identifying altered RNA splicing or expression. A marker can be derived from expressed nucleotide sequences (e.g., from an RNA, mRNA, a cDNA, etc.), or from an encoded polypeptide.
In some embodiments, a biomarker disclosed herein comprises at least one RNA biomarker.
In some embodiments, at least one RNA biomarker having an increased expression, having a reduced expression, having an increased exon skipping, having a reduced exon skipping, having an increased mutually exclusive exon switching, having a reduced mutually exclusive exon switching, having an increased alternative 5′ splicing, having a reduced alternative 5′ splicing, having an increased alternative 3′ splicing or having a reduced alternative 3′ splicing, in the biological sample, relative to a control sample, is indicative of the subject as having, or having a propensity to develop, a fragile X-associated disorder (e.g., FXS).
In certain embodiments, at least one RNA biomarker having an increased expression, having a reduced expression, having an increased exon skipping, having a reduced exon skipping, having an increased mutually exclusive exon switching, having a reduced mutually exclusive exon switching, having an increased alternative 5′ splicing, having a reduced alternative 5′ splicing, having an increased alternative 3′ splicing or having a reduced alternative 3′ splicing, relative to a control sample, is indicative of the subject as having a propensity to have a poorer prognosis of a fragile X-associated disorder (e.g., FXS).
In certain embodiments, at least one RNA biomarker having an increased expression, having a reduced expression, having an increased exon skipping, having a reduced exon skipping, having an increased mutually exclusive exon switching, having a reduced mutually exclusive exon switching, having an increased alternative 5′ splicing, having a reduced alternative 5′ splicing, having an increased alternative 3′ splicing or having a reduced alternative 3′ splicing, relative to a control sample, is indicative of the subject as having a propensity to have a poorer treatment outcome for a fragile X-associated disorder (e.g., FXS).
In some embodiments, the at least one RNA biomarker of the disclosure is AGAP1, RAB25, FAM3B, XKR3, MAP3K15, LEP, RP11-706O15.3, GCOM1, CXCL6, RGL3, NECAB2, TGM3, LRRC6, MAB21L3, RP11-36B15.1, AC091878.1, RP11-154H23.3, NOV, AC093495.4, RP11-455F5.6, RGPD2, COL9A3, CLEC18A, RP11-256L6.2, LINC01127, SLC38A11, EFCAB12, LA16c-380H5.5, CXCL1, RP11-1334A24.5, AC100793.2, ANKDD1A, AVIL, RP11-44F14.8, RP11-290F20.1, AC116366.5, EPHB4, ST6GALNAC3, PANX2, CREB5, KIAA0319, HECW2, ADCY4, LINC00173, RP11-59D5_B.2, RP11-274B18.2, RP11-213H15.3, CORO7-PAM16, HAL, DPEP3, AC002467.7, MGAM, PNMA8A, FMR1, S100B, RP11-885N19.6, RP11-545I5.3, AC091814.2, KLRC2, L1TD1, PGBD5, MXRA7, CROCC2, SEMA5A, PLA2G4C, RP11-1008C21.1, TANC1, C4orf50, NUAK1, AC104809.4, RGS17, KCNS1, DRAXIN, B3GAT1, ARHGEF28, KIF19, APOL4, GZMH, GAS1, SCD5, GLB1L2, IGHA1, KNDC1, RP11-383H13.1, FGFR2, TFCP2L1, PDGFRB, LAG3, GPR153, PODN, CKB, CERCAM, ZNF365, JUP, TRNP1, JAKMIP1, CPXM1, SLC1A7, LGR6, FCRL6, MORN4, TUBB2A, PRSS23, BFSP1, NCALD, ZNF573, PAK1, MIR4435-2HG, CD8B, PDGFC, TRAPPC2L, AC006504.5, ZNF512, FAM228B, NEIL2, FAM78A, FYB1, RNF216P1, ZCWPW1, DTX2, ATP5MD, MX2, LYRM1, GUF1, DPH7, NSFL1C, MTMR1, GTPBP10, RGS3, DRAM2, RHOH, LAIR2, GBP3, GTF2H1, XPNPEP3, ZNF888, TBC1D5, AC060780.1, SDHAP2, KMT2A, SH3BP2, CSNK1G2, NSUN5P1, LINC01128, RNF19A, SNHG8, TOP1MT, AL135818.1, CR1, CRIM1, NAP1L1, AC004593.2, SEC61A2, PCNX2, TPT1-AS1, HLA-A, LUCAT1, PTPN2, SEC31B, POLR2J3, POLR2J4, CAST, POLR2J4, NUMBL, PRMT7, ATF7IP2, TIMM23B-AGAP6, ADGRE2, GTF2H2B, MICA, SLC29A2, ZBTB10, NLGN3, METTL25, ADAM15, SSH1, SIRPB1, PARP2, PACRGL, ENTPD1-AS1, FUZ, SDR39U1, EPOR, ZSCAN26, SNHG17, GPS2, NECAP1, MRPL11, DNAJC19, ANKZF1, C1orf162, PIGT, SLC25A37, AP1G1, CIC, ITGB7, ATG16L2, BECN1, ARHGEF40, BANP, PIGA, RAD52, IRF3, CEP78, SPINT1, TMEM156, NT5C3B, PLD2, ANKRD12, CASP8, PACS2, HLA-DMA, DHPS, PDCD6, SNX5, MPPE1, AC016394.2, DPM1, E2F5, PTPN7, MTFP1, TOR1AIP1, POT1, JOSD2, NLRX1, FDXR, ZDHHC16, ALKBH4, RPS9, ZNF302, TENT4B, TKT, CARD8, RBM26, WSB1, DDX60L, ATP11A, SRGAP2, CEACAM21, COX18, WDR47, PATZ1, POLM, CC2D1B, CLK4, MIB2, PHF1, KANSL1 or TCF3, or a combination thereof.
In particular embodiments, the at least one RNA biomarker comprises fragile X messenger ribonucleoprotein 1 (FMR1).
In some embodiments, the method comprises assaying at least 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, 40 or 45 RNA markers in the biological sample from the subject. Non-limiting examples of RNA biomarkers having an increased expression, having a reduced expression, having an increased exon skipping, having a reduced exon skipping, having an increased mutually exclusive exon switching, having a reduced mutually exclusive exon switching, having an increased alternative 5′ splicing, having a reduced alternative 5′ splicing, having an increased alternative 3′ splicing or having a reduced alternative 3′ splicing, or a combination thereof, can be found in Tables 1-10.
Increased RNA Expression In some embodiments, at least one RNA biomarker (e.g., at least: 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 25 RNA biomarkers) having an increased expression in the biological sample, relative to a control sample, is indicative of the subject as having, or having a propensity to develop, a fragile X-associated disorder (e.g., FXS).
In certain embodiments, at least one RNA biomarker (e.g., at least: 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 25 RNA biomarkers) having an increased expression in the biological sample, relative to a control sample, is indicative of the subject as having a propensity to have a poorer prognosis of a fragile X-associated disorder (e.g., FXS).
In certain embodiments, at least one RNA biomarker (e.g., at least: 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 25 RNA biomarkers) having an increased expression in the biological sample, relative to a control sample, is indicative of the subject as having a propensity to have a poorer treatment outcome for a fragile X-associated disorder (e.g., FXS).
In certain embodiments, expression of the at least one RNA biomarker has a log 2 fold increase of at least about 0.50 in the biological sample, relative to a control sample, for example, the log 2 fold increase is at least about 0.55, 0.60, 0.65, 0.70, 0.75, 0.80, 0.85, 0.90, 0.95, 1.00, 1.25, 1.50, 1.75, 2.00, 2.25, 2.50, 2.75, 3.00, 3.25, 31.50, 3.75, 4.00, 4.25, 4.50, 4.75, 5.00, 5.25, 5.50, 5.75, or 6.00. In particular embodiments, expression of the at least one RNA biomarker has a log 2 fold increase of ≥0.80 in the biological sample, relative to a control sample, optionally, wherein the log 2 fold increase is ≥0.95.
In some embodiments, expression of the at least one RNA biomarker has a log 2 fold increase of about 0.50-10.00 in the biological sample, relative to a control sample, for example, about: 0.55-10.00, 0.55-9.50, 0.60-9.50, 0.60-9.00, 0.65-9.00, 0.65-8.50, 0.70-8.50, 0.70-8.00, 0.75-8.00, 0.75-7.50, 0.80-7.50, 0.80-7.00, 0.85-7.00, 0.85-6.50, 0.90-6.50, 0.90-6.00, 0.95-6.00 or 0.95-5.95.
Non-limiting examples of RNA biomarkers having increased expression in a biological sample, relative to a control sample, can be found in Table 1.
In some embodiments, the at least one RNA biomarker is AGAP1, RAB25, FAM3B, XKR3, MAP3K15, LEP, RP11-706O15.3, GCOM1, CXCL6, RGL3, NECAB2, TGM3, LRRC6, MAB21L3, RP11-36B15.1, AC091878.1, RP11-154H23.3, NOV, AC093495.4, RP11-455F5.6, RGPD2, COL9A3, CLEC18A, RP11-256L6.2, LINC01127, SLC38A11, EFCAB12, LA16c-380H5.5, CXCL1, RP11-1334A24.5, AC100793.2, ANKDD1A, AVIL, RP11-44F14.8, RP11-290F20.1, AC116366.5, EPHB4, ST6GALNAC3, PANX2, CREB5, KIAA0319, HECW2, ADCY4, LINC00173, RP11-59D5_B.2, RP11-274B18.2, RP11-213H15.3, CORO7-PAM16, HAL, DPEP3, AC002467.7, MGAM or PNMA8A, or a combination thereof.
In particular embodiments, the at least one RNA biomarker comprises isoform 12 of FMR1.
Reduced RNA Expression In some embodiments, at least one RNA biomarker (e.g., at least: 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 25 RNA biomarkers) having a reduced expression in the biological sample, relative to a control sample, is indicative of the subject as having, or having a propensity to develop, a fragile X-associated disorder (e.g., FXS).
In certain embodiments, at least one RNA biomarker (e.g., at least: 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 25 RNA biomarkers) having a reduced expression in the biological sample, relative to a control sample, is indicative of the subject as having a propensity to have a poorer prognosis of a fragile X-associated disorder (e.g., FXS).
In certain embodiments, at least one RNA biomarker (e.g., at least: 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 25 RNA biomarkers) having a reduced expression in the biological sample, relative to a control sample, is indicative of the subject as having a propensity to have a poorer treatment outcome for a fragile X-associated disorder (e.g., FXS).
In certain embodiments, expression of the at least one RNA biomarker has a log 2 fold reduction of at least about 0.50 in the biological sample, relative to a control sample, for example, the log 2 fold reduction is at least about 0.55, 0.60, 0.65, 0.70, 0.75, 0.80, 0.85, 0.90, 0.95, 1.00, 1.25, 1.50, 1.75, 2.00, 2.25, 2.50, 2.75, 3.00, 3.25, 31.50, 3.75, 4.00, 4.25, 4.50, 4.75, 5.00, 5.25, 5.50, 5.75, or 6.00. In particular embodiments, expression of the at least one RNA biomarker has a log 2 fold reduction of ≥1.00 in the biological sample, relative to a control sample, optionally, wherein the log 2 fold reduction is ≥1.16.
In some embodiments, expression of the at least one RNA biomarker has a log 2 fold reduction of about 0.50-7.00 in the biological sample, relative to a control sample, for example, about: 0.50-6.50, 0.55-6.50, 0.55-6.00, 0.60-6.00, 0.60-5.50, 0.65-5.50, 0.65-5.00, 0.70-5.00, 0.70-4.60, 0.75-4.60, 0.75-4.40, 0.80-4.40, 0.80-4.20, 0.85-4.20, 0.85-4.10, 0.90-4.10, 0.90-4.00, 0.95-4.00, 0.95-3.90, 1.00-3.90, 1.00-3.80, 1.05-3.80, 1.05-3.70, 1.10-3.70, 1.10-3.60, 1.15-3.60 or 1.15-3.00.
Non-limiting examples of RNA biomarkers having reduced expression in a biological sample, relative to a control sample, can be found in Table 2.
In some embodiments, the at least one RNA biomarker is FMR1, S100B, RP11-885N19.6, RP11-545I5.3, AC091814.2, KLRC2, L1TD1, PGBD5, MXRA7, CROCC2, SEMA5A, PLA2G4C, RP11-1008C21.1, TANC1, C4orf50, NUAK1, AC104809.4, RGS17, KCNS1, DRAXIN, B3GAT1, ARHGEF28, KIF19, APOL4, GZMH, GAS1, SCD5, GLB1L2, IGHA1, KNDC1, RP11-383H13.1, FGFR2, TFCP2L1, PDGFRB, LAG3, GPR153, PODN, CKB, CERCAM, ZNF365, JUP, TRNP1, JAKMIP1, CPXM1, SLC1A7, LGR6, FCRL6, MORN4, TUBB2A, PRSS23 or BFSP1, or a combination thereof.
In particular embodiments, the at least one RNA biomarker comprises isoform 1 of FMR1.
Increased Exon Skipping In some embodiments, at least one RNA biomarker (e.g., at least: 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 25 RNA biomarkers) having an increased exon skipping in the biological sample, relative to a control sample, is indicative of the subject as having, or having a propensity to develop, a fragile X-associated disorder (e.g., FXS).
In certain embodiments, at least one RNA biomarker (e.g., at least: 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 25 RNA biomarkers) having an increased exon skipping in the biological sample, relative to a control sample, is indicative of the subject as having a propensity to have a poorer prognosis of a fragile X-associated disorder (e.g., FXS).
In certain embodiments, at least one RNA biomarker (e.g., at least: 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 25 RNA biomarkers) having an increased exon skipping in the biological sample, relative to a control sample, is indicative of the subject as having a propensity to have a poorer treatment outcome for a fragile X-associated disorder (e.g., FXS).
In certain embodiments, exon skipping of the at least one RNA biomarker is increased by at least about 5% in the biological sample, relative to a control sample, for example, at least about: 6%, 7%, 8%, 9%, 10%, 12%, 15%, 18%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85% or 90%. In particular embodiments, the increase is at least about 13.0%, optionally, the increase is at least about 16.0%.
In some embodiments, exon skipping of the at least one RNA biomarker is increased by about 5-90% in the biological sample, relative to a control sample, for example, about: 6-90%, 6-85%, 7-85%, 7-80%, 8-80%, 8-75%, 9-75%, 9-70%, 10-70%, 10-68%, 11-68%, 11-65%, 12-65%, 12-62%, 13-62%, 13-60%, 14-60%, 14-58%, 15-58%, 15-55% or 16-55%.
Non-limiting examples of RNA biomarkers having increased exon skipping in a biological sample, relative to a control sample, can be found in Table 4.
In some embodiments, the at least one RNA biomarker is NCALD, ZNF573, PAK1, MIR4435-2HG, CD8B, PDGFC, TRAPPC2L, AC006504.5, ZNF512, FAM228B, NEIL2, FAM78A, FYB1, RNF216P1, ZCWPW1, DTX2, ATP5MD, MX2, LYRM1, GUF1, DPH7, NSFL1C, MTMR1, GTPBP10 or RGS3, or a combination thereof.
Reduced Exon Skipping In some embodiments, at least one RNA biomarker (e.g., at least: 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 25 RNA biomarkers) having a reduced exon skipping in the biological sample, relative to a control sample, is indicative of the subject as having, or having a propensity to develop, a fragile X-associated disorder (e.g., FXS).
In certain embodiments, at least one RNA biomarker (e.g., at least: 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 25 RNA biomarkers) having a reduced exon skipping in the biological sample, relative to a control sample, is indicative of the subject as having a propensity to have a poorer prognosis of a fragile X-associated disorder (e.g., FXS).
In certain embodiments, at least one RNA biomarker (e.g., at least: 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 25 RNA biomarkers) having a reduced exon skipping in the biological sample, relative to a control sample, is indicative of the subject as having a propensity to have a poorer treatment outcome for a fragile X-associated disorder (e.g., FXS).
In certain embodiments, exon skipping of the at least one RNA biomarker is reduced by at least about 5% in the biological sample, relative to a control sample, for example, at least about: 6%, 7%, 8%, 9%, 10%, 12%, 15%, 18%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85% or 90%. In particular embodiments, the reduction is at least about 13.0%, optionally, the reduction is at least about 17.0%.
In some embodiments, exon skipping of the at least one RNA biomarker is reduced by about 5-90% in the biological sample, relative to a control sample, for example, about: 6-90%, 6-85%, 7-85%, 7-80%, 8-80%, 8-75%, 9-75%, 9-70%, 10-70%, 10-68%, 11-68%, 11-65%, 12-65%, 12-62%, 13-62%, 13-60%, 14-60%, 14-58%, 15-58%, 15-55%, 16-55% or 17-55%.
Non-limiting examples of RNA biomarkers having reduced exon skipping in a biological sample, relative to a control sample, can be found in Table 3.
In some embodiments, the at least one RNA biomarker is NCALD, DRAM2, RHOH, LAIR2, GBP3, GTF2H1, XPNPEP3, ZNF888, TBC1D5, AC060780.1, SDHAP2, KMT2A, SH3BP2, CSNK1G2, ATP5MD, NSUN5P1, LINC01128, RNF19A, SNHG8, TOP1MT or AL135818.1, or a combination thereof.
Increased Mutually Exclusive Exon Switching In some embodiments, at least one RNA biomarker (e.g., at least: 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 25 RNA biomarkers) having an increased mutually exclusive exon switching in the biological sample, relative to a control sample, is indicative of the subject as having, or having a propensity to develop, a fragile X-associated disorder (e.g., FXS). Mutually exclusive splicing generates alternative isoforms by retaining only one exon of a cluster of neighboring internal exons in the mature transcript and is a way to modulate protein function. See, e.g., Hatje et al., Mol Syst Biol. 13(12):959 (2017), Letunic et al., Hum Mol Genet. 11(13):1561-7 (2002), Meijers et al., Nature 449(7161):487-91 (2007), Pohl et al., Biosystems 114(1):31-8 (2013) and Tress et al., Trends Biochem Sci. 42(2):98-110 (2017).
In certain embodiments, at least one RNA biomarker (e.g., at least: 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 25 RNA biomarkers) having an increased mutually exclusive exon switching in the biological sample, relative to a control sample, is indicative of the subject as having a propensity to have a poorer prognosis of a fragile X-associated disorder (e.g., FXS).
In certain embodiments, at least one RNA biomarker (e.g., at least: 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 25 RNA biomarkers) having an increased mutually exclusive exon switching in the biological sample, relative to a control sample, is indicative of the subject as having a propensity to have a poorer treatment outcome for a fragile X-associated disorder (e.g., FXS).
In certain embodiments, mutually exclusive exon switching of the at least one RNA biomarker is increased by at least about 5% in the biological sample, relative to a control sample, for example, at least about: 6%, 7%, 8%, 9%, 10%, 12%, 15%, 18%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85% or 90%. In particular embodiments, the increase is at least about 10.0%, optionally, the increase is at least about 13.0%.
In some embodiments, mutually exclusive exon switching of the at least one RNA biomarker is increased by about 5-90% in the biological sample, relative to a control sample, for example, about: 5-85%, 6-85%, 6-80%, 7-80%, 7-75%, 8-75%, 8-70%, 9-70%, 9-65%, 10-65%, 10-60%, 11-60%, 11-55%, 12-55%, 12-50%, 13-50%, 13-45%, 14-45% or 14-40%.
Non-limiting examples of RNA biomarkers having increased mutually exclusive exon switching in a biological sample, relative to a control sample, can be found in Table 6.
In some embodiments, the at least one RNA biomarker is CR1, CRIM1, ZCWPW1, NAP1L1, TBC1D5, MIR4435-2HG, AC004593.2, GBP3, SEC61A2, PCNX2, TPT1-AS1, HLA-A, LUCAT1, PTPN2, SEC31B, POLR2J3, POLR2J4, CAST, NUMBL, PRMT7, ATF7IP2 or TIMM23B-AGAP6, or a combination thereof.
Reduced Mutually Exclusive Exon Switching In some embodiments, at least one RNA biomarker (e.g., at least: 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 25 RNA biomarkers) having a reduced mutually exclusive exon switching in the biological sample, relative to a control sample, is indicative of the subject as having, or having a propensity to develop, a fragile X-associated disorder (e.g., FXS).
In certain embodiments, at least one RNA biomarker (e.g., at least: 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 25 RNA biomarkers) having a reduced mutually exclusive exon switching in the biological sample, relative to a control sample, is indicative of the subject as having a propensity to have a poorer prognosis of a fragile X-associated disorder (e.g., FXS).
In certain embodiments, at least one RNA biomarker (e.g., at least: 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 25 RNA biomarkers) having a reduced mutually exclusive exon switching in the biological sample, relative to a control sample, is indicative of the subject as having a propensity to have a poorer treatment outcome for a fragile X-associated disorder (e.g., FXS).
In certain embodiments, mutually exclusive exon switching of the at least one RNA biomarker is reduced by at least about 5% in the biological sample, relative to a control sample, for example, at least about: 6%, 7%, 8%, 9%, 10%, 12%, 15%, 18%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85% or 90%. In particular embodiments, the reduction is at least about 12.0%, optionally, the increase is at least about 15.0%.
In some embodiments, mutually exclusive exon switching of the at least one RNA biomarker is reduced by about 5-90% in the biological sample, relative to a control sample, for example, about: 5-88%, 6-88%, 6-85%, 7-85%, 7-82%, 8-82%, 8-80%, 9-78%, 9-75%, 10-75%, 10-72%, 11-72%, 11-70%, 12-70%, 12-68%, 13-68%, 13-65%, 14-65%, 14-62%, 15-62% or 15-60%.
Non-limiting examples of RNA biomarkers having reduced mutually exclusive exon switching in a biological sample, relative to a control sample, can be found in Table 5.
In some embodiments, the at least one RNA biomarker is HLA-A, ADGRE2, PAK1, TBC1D5, GTF2H2B, MICA, SLC29A2, ZBTB10, NLGN3, CAST, METTL25, ADAM15, LUCAT1, SSH1, SIRPB1 or GBP3, or a combination thereof.
Increased Alternative 5′ Splicing In some embodiments, at least one RNA biomarker (e.g., at least: 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 25 RNA biomarkers) having an increased alternative 5′ splicing in the biological sample, relative to a control sample, is indicative of the subject as having, or having a propensity to develop, a fragile X-associated disorder (e.g., FXS).
In certain embodiments, at least one RNA biomarker (e.g., at least: 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 25 RNA biomarkers) having an increased alternative 5′ splicing in the biological sample, relative to a control sample, is indicative of the subject as having a propensity to have a poorer prognosis of a fragile X-associated disorder (e.g., FXS).
In certain embodiments, at least one RNA biomarker (e.g., at least: 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 25 RNA biomarkers) having an increased alternative 5′ splicing in the biological sample, relative to a control sample, is indicative of the subject as having a propensity to have a poorer treatment outcome for a fragile X-associated disorder (e.g., FXS).
In certain embodiments, alternative 5′ splicing of the at least one RNA biomarker is increased by at least about 2.0% in the biological sample, relative to a control sample, for example, at least about: 2.5%, 3.0%, 3.5%, 4.0%, 4.5%, 5.0%, 52.5%, 6.0%, 6.5%, 7.0%, 7.5%, 8.0%, 8.5%, 9.0%, 9.5%, 10%, 12%, 15%, 18%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85% or 90%. In particular embodiments, the increase is at least about 4.5%, optionally, the increase is at least about 5.0%.
In some embodiments, alternative 5′ splicing of the at least one RNA biomarker is increased by about 2.0-65% in the biological sample, relative to a control sample, for example, about: 2.5-65%, 2.5-60%, 3.0-60%, 3.0-55%, 3.5-55%, 3.5-50%, 4.0-50%, 4.0-45%, 4.5-45%, 4.5-40%, 5.0-40% or 5.0-35%.
Non-limiting examples of RNA biomarkers having increased alternative 5′ splicing in a biological sample, relative to a control sample, can be found in Table 8.
In some embodiments, the at least one RNA biomarker is PARP2, PACRGL, ENTPD1-AS1, NEIL2, FUZ, SDR39U1, ADAM15, EPOR, ZSCAN26, SNHG17, GPS2, NECAP1, MRPL11, DNAJC19, ANKZF1, C1orf162, PIGT, SLC25A37, AP1G1, CIC, ITGB7, ATG16L2, BECN1 or ARHGEF40, or a combination thereof.
Reduced Alternative 5′ Splicing In some embodiments, at least one RNA biomarker (e.g., at least: 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 25 RNA biomarkers) having a reduced alternative 5′ splicing in the biological sample, relative to a control sample, is indicative of the subject as having, or having a propensity to develop, a fragile X-associated disorder (e.g., FXS).
In certain embodiments, at least one RNA biomarker (e.g., at least: 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 25 RNA biomarkers) having a reduced alternative 5′ splicing in the biological sample, relative to a control sample, is indicative of the subject as having a propensity to have a poorer prognosis of a fragile X-associated disorder (e.g., FXS).
In certain embodiments, at least one RNA biomarker (e.g., at least: 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 25 RNA biomarkers) having a reduced alternative 5′ splicing in the biological sample, relative to a control sample, is indicative of the subject as having a propensity to have a poorer treatment outcome for a fragile X-associated disorder (e.g., FXS).
In certain embodiments, alternative 5′ splicing of the at least one RNA biomarker is reduced by at least about 2.0% in the biological sample, relative to a control sample, for example, at least about: 2.5%, 3.0%, 3.5%, 4.0%, 4.5%, 5.0%, 52.5%, 6.0%, 6.5%, 7.0%, 7.5%, 8.0%, 8.5%, 9.0%, 9.5%, 10%, 12%, 15%, 18%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85% or 90%. In particular embodiments, the reduction is at least about 4.5%, optionally, the increase is at least about 5.5%.
In some embodiments, alternative 5′ splicing of the at least one RNA biomarker is reduced by about 2.0-65% in the biological sample, relative to a control sample, for example, about: 2.5-65%, 2.5-60%, 3.0-60%, 3.0-55%, 3.5-55%, 3.5-50%, 4.0-50%, 4.0-45%, 4.5-45%, 4.5-40%, 5.0-40%, 5.0-35%, 5.5-35% or 5.5-30%.
Non-limiting examples of RNA biomarkers having reduced alternative 5′ splicing in a biological sample, relative to a control sample, can be found in Table 7.
In some embodiments, the at least one RNA biomarker is BANP, PIGA, SNHG8, RAD52, IRF3, CEP78, SPINT1, TMEM156, NT5C3B, PLD2, HLA-A, ANKRD12, CASP8, PACS2, HLA-DMA, DHPS or PDCD6, or a combination thereof.
Increased Alternative 3′ Splicing In some embodiments, at least one RNA biomarker (e.g., at least: 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 25 RNA biomarkers) having an increased alternative 3′ splicing in the biological sample, relative to a control sample, is indicative of the subject as having, or having a propensity to develop, a fragile X-associated disorder (e.g., FXS).
In certain embodiments, at least one RNA biomarker (e.g., at least: 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 25 RNA biomarkers) having an increased alternative 3′ splicing in the biological sample, relative to a control sample, is indicative of the subject as having a propensity to have a poorer prognosis of a fragile X-associated disorder (e.g., FXS).
In certain embodiments, at least one RNA biomarker (e.g., at least: 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 25 RNA biomarkers) having an increased alternative 3′ splicing in the biological sample, relative to a control sample, is indicative of the subject as having a propensity to have a poorer treatment outcome for a fragile X-associated disorder (e.g., FXS).
In certain embodiments, alternative 3′ splicing of the at least one RNA biomarker is increased by at least about 2.0% in the biological sample, relative to a control sample, for example, at least about: 2.5%, 3.0%, 3.5%, 4.0%, 4.5%, 5.0%, 52.5%, 6.0%, 6.5%, 7.0%, 7.5%, 8.0%, 8.5%, 9.0%, 9.5%, 10%, 12%, 15%, 18%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85% or 90%. In particular embodiments, the increase is at least about 6.5%, optionally, the increase is at least about 7.5%.
In some embodiments, alternative 3′ splicing of the at least one RNA biomarker is increased by about 5.0-90% in the biological sample, relative to a control sample, for example, about: 5.0-85%, 5.2-85%, 5.2-80%, 5.5-80%, 5.5-75%, 5.8-75%, 5.8-70%, 6.0-70%, 6.0-65%, 6.2-65%, 6.2-60%, 6.5-60%, 6.5-55%, 6.8-55%, 6.8-50%, 7.0-50%, 7.0-45%, 7.2-45%, 7.2-40% or 7.5-40%.
Non-limiting examples of RNA biomarkers having increased alternative 3′ splicing in a biological sample, relative to a control sample, can be found in Table 10.
In some embodiments, the at least one RNA biomarker is SNX5, POLR2J3, MPPE1, AC016394.2, DPM1, E2F5, PTPN7, MTFP1, TOR1AIP1, POT1, JOSD2, NLRX1, FDXR, ZDHHC16, ALKBH4, RPS9, ZNF302, TENT4B, ADGRE2, TKT, CARD8, RBM26 or WSB1, or a combination thereof.
Reduced Alternative 3′ Splicing In some embodiments, at least one RNA biomarker (e.g., at least: 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 25 RNA biomarkers) having a reduced alternative 3′ splicing in the biological sample, relative to a control sample, is indicative of the subject as having, or having a propensity to develop, a fragile X-associated disorder (e.g., FXS).
In certain embodiments, at least one RNA biomarker (e.g., at least: 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 25 RNA biomarkers) having a reduced alternative 3′ splicing in the biological sample, relative to a control sample, is indicative of the subject as having a propensity to have a poorer prognosis of a fragile X-associated disorder (e.g., FXS).
In certain embodiments, at least one RNA biomarker (e.g., at least: 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or 25 RNA biomarkers) having a reduced alternative 3′ splicing in the biological sample, relative to a control sample, is indicative of the subject as having a propensity to have a poorer treatment outcome for a fragile X-associated disorder (e.g., FXS).
In certain embodiments, alternative 3′ splicing of the at least one RNA biomarker is reduced by at least about 2.0% in the biological sample, relative to a control sample, for example, at least about: 2.5%, 3.0%, 3.5%, 4.0%, 4.5%, 5.0%, 52.5%, 6.0%, 6.5%, 7.0%, 7.5%, 8.0%, 8.5%, 9.0%, 9.5%, 10%, 12%, 15%, 18%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85% or 90%. In particular embodiments, the reduction is at least about 4.0%, optionally, the increase is at least about 5.0%.
In some embodiments, alternative 3′ splicing of the at least one RNA biomarker is reduced by about 2.0-65% in the biological sample, relative to a control sample, for example, about: 2.5-65%, 2.5-60%, 3.0-60%, 3.0-55%, 3.5-55%, 3.5-50%, 4.0-50%, 4.0-45%, 4.5-45%, 4.5-40%, 5.0-40% or 5.0-35%.
Non-limiting examples of RNA biomarkers having reduced alternative 3′ splicing in a biological sample, relative to a control sample, can be found in Table 9.
In some embodiments, the at least one RNA biomarker is DDX60L, ATP11A, SRGAP2, CEACAM21, COX18, WDR47, PATZ1, POLM, CC2D1B, CLK4, MIB2, PHF1, KANSL1 or TCF3, or a combination thereof.
Assaying Biomarkers The level or splicing of a RNA biomarker can be measured using any technique suitable for detecting RNA expression level or expression pattern in a biological sample. For example, by performing northern blot analysis, in situ hybridization, quantitative reverse transcriptase polymerase chain reaction (RT-qPCR), a microarray assay, cDNA sequencing (RNA-Seq, Drop-Seq, CEL-seq2, MARS-seq, SCRB-seq, Smart-seq, and Smart-seq2), flow cytometry, or a combination thereof. See, e.g., www.illumina.com/science/sequencing-method-explorer/kits-and-arrays/drop-seq.html, Macosko et al., Cell 161(5):1202-14 (2015) and Ziegenhain et al., Mol Cell 65(4):631-43 (2017). In some embodiments, the level or splicing of the at least one RNA biomarker is measured using a microarray assay.
Primers for amplifying and/or sequencing biomarkers of the disclosure and suitable probes for detecting such biomarkers can be designed using conventional methodology by those skilled in the art.
In particular embodiments, the level or splicing of a RNA biomarker is measured indirectly, at the protein level, using any technique known in the art. For example, by performing enzyme-linked immunoassay (ELISA) or Western blotting.
In some embodiments, the level and/or splicing of the at least one RNA biomarker in the sample is compared to that in a control sample or a reference standard.
In some embodiments, the control sample comprises tissue or blood from an unaffected subject or a population of unaffected subjects. An unaffected subject is a healthy subject, a subject who is not diagnosed with a fragile X-associated disorder (e.g., FXS) or a subject who does not have a fragile X-associated disorder (e.g., FXS). In some embodiments, the control sample (e.g., tissue or blood sample) is processed along with the sample from the subject. In other embodiments, the control sample is processed separately (e.g., at an earlier or a later time) from the test sample.
The term “reference standard” can be, for example, a mean, an average, a numerical mean or range of numerical means, a numerical pattern, a graphical pattern or the corresponding RNA expression or splicing level derived from a reference subject (e.g., an unaffected subject) or reference population (e.g., a population of unaffected subjects).
In some embodiments, the control sample is from a sample from a typically developing subject, e.g., from an age-matched sample from a typically developing subject. In certain embodiments, the control sample is a theoretical value calculated from the general population. In particular embodiments, the control sample is a baseline sample of the subject, e.g., at an earlier age or before treatment.
Subjects The term “subject” refers to a mammalian subject, preferably human, diagnosed with or suspected of having a fragile X-associated disorder (e.g., FXS).
In some embodiments, the subject has one X chromosome and one Y chromosome. In some embodiments, the subject has two X chromosomes. In certain embodiments, the subject has two X chromosomes and one Y chromosome. In particular embodiments, the subject has one X chromosome and two Y chromosomes.
In some embodiments, the subject is a human male. In some embodiments the subject is human female.
In some embodiments, the subject is at least about 1 month of age, for example, at least about 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 15, 18 or 21 months of age, or at least about: 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 years of age. In some embodiments, the subject is about: 1-100, 1-80, 1-60, 1-30, 1-24, 1-20, 1-18, 1-12, 1-10, 1-8, 1-6, 2-100, 2-80, 2-60, 2-30, 2-24, 2-20, 2-18, 2-12, 2-10, 2-8, 2-6, 3-100, 3-80, 3-60, 3-30, 3-24, 3-20, 3-18, 3-12, 3-10, 3-8, 3-6, 4-100, 4-80, 4-60, 4-30, 4-24, 4-20, 4-18, 4-12, 4-10, 4-8, 4-6, 5-100, 5-80, 5-60, 5-30, 5-24, 5-20, 5-18, 5-12, 5-10, 5-8, 6-100, 6-80, 6-60, 6-30, 6-24, 6-20, 6-18, 6-12, 6-10, 8-100, 8-80, 8-60, 8-30, 8-24, 8-20, 8-18, 8-12, 10-100, 10-80, 10-60, 10-30, 10-24, 10-20, 10-18, 12-100, 12-80, 12-38, 12-60, 12-50, 12-40, 12-30, 12-24, 12-20, 12-18, 18-100, 18-80, 18-60, 18-50, 18-40, 18-30, 18-24, 20-100, 20-80, 20-60, 20-50, 20-40, 20-30, 20-25, 30-100, 30-80, 30-60, 30-55, 30-50, 30-45, 30-40, 40-100, 40-80, 40-60, 40-55 or 40-50 years of age. In some embodiments, the subject is about 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 55, 60, 65, 70, 75, 80 or 100 years of age. In other embodiments, the subject is a fetus. In some embodiments, the subject is a neonatal subject.
In some embodiments, the subject is 18 years of age or older, e.g., 18 to less than 40 years of age, 18 to less than 45 years of age, 18 to less than 50 years of age, 18 to less than 55 years of age, 18 to less than 60 years of age, 18 to less than 65 years of age, 18 to less than 70 years of age, 18 to less than 75 years of age, 40 to less than 75 years of age, 45 to less than 75 years of age, 50 to less than 75 years of age, 55 to less than 75 years of age, 60 to less than 75 years of age, 65 to less than 75 years of age, 60 to less than 75 years of age, 40 years of age or older, 45 years of age or older, 50 years of age or older, 55 years of age or older, 60 years of age or older, 65 years of age or older, 70 years of age or older, 75 years of age or older or 100 years of age or older. In some embodiments, the subject is a child. In some embodiments, the subject is 18 years of age or younger, e.g., 0-18 years of age, 0-12 years of age, 0-16 years of age, 0-17 years of age, 2-12 years of age, 2-16 years of age, 2-17 years of age, 2-18 years of age, 3-12 years of age, 3-16 years of age, 3-17 years of age, 3-18 years of age, 4-12 years of age, 4-16 years of age, 4-17 years of age, 4-18 years of age, 6-12 years of age, 6-16 years of age, 6-17 years of age, 6-18 years of age, 9-12 years of age, 9-16 years of age, 9-17 years of age, 9-18 years of age, 12-16 years of age, 12-17 years of age or 12-18 years of age.
In some embodiments, the subject has one or more of the physical and/or medical features associated with a fragile X-associated disorder (e.g., FXS). Non-limiting examples of physical features associated with FXS include a long face, prominent ears and chin, arched palate, large testicles at puberty, low muscle tone, flat feet, and hyperextensible joints. Non-limiting examples of medical or behavioral features associated with FXS include sleep problems, seizures, recurrent ear infections, mitral valve prolapse, behaviors of hyperactivity, short attention span, hand biting or hand flapping, poor eye contact and social skills, shyness, anxiety, autism, epilepsy, aggression, delayed speech and motor development, repetitive speech, sensitivity to sensory stimulation (including a hypersensitivity to being touched, to light or to sound). In certain embodiments, the subject is a female with an IQ score of less than 115, 110, 105, 100, 95 or 90. In particular embodiments, the subject is a male with an IQ score of less than 60, 55, 50 or 45.
In certain embodiments, the subject has one or more of the following: irregular menses, fertility problem, elevated FSH (follicle-stimulating hormone) level, premature ovarian failure, primary ovarian insufficiency, and vasomotor symptoms (e.g., “hot flash”). In some embodiments, the subject has one or more of the following: intention tremor, parkinsonism, ataxia, memory loss, white matter lesion involving middle cerebellar peduncles, and cognitive decline.
Treatments In some embodiments, the method further comprises treating the subject if the subject is diagnosed to have, or has a propensity to develop, a fragile X-associated disorder (e.g., FXS).
“Treat,” “treating” or “treatment” refers to therapeutic treatment wherein the objective is to slow down (lessen) an undesired physiological change or disease, such as the development or progression of the fragile X-associated disorder (e.g., FXS), or to provide a beneficial or desired clinical outcome during treatment. Beneficial or desired clinical outcomes include alleviation of symptoms, diminishment of extent of disease, stabilized (i.e., not worsening) state of disease, delay or slowing of disease progression, amelioration or palliation of the disease state, whether detectable or undetectable.
Non-limiting examples of symptoms include speech and motor development symptoms, cognitive disabilities, including learning and intellectual disabilities, hyperactivity, short attention span, anxiety, sensitivity to sensory stimulation, sleep problems, seizures, recurrent ear infections, and mitral valve prolapse.
In some embodiments, treating the subject comprises administering a therapeutic, providing the subject with a specific diet, or a combination thereof. Non-limiting examples of the therapeutics include metabotropic glutamate receptor 5 (mGluR5) modulator (e.g., Basimglurant or Mavoglurant), GABAB receptor activator (e.g., arbaclofen), GABAA or GABAB receptor activator (e.g., acamprosate), AMPAkine (e.g., AX516), CB1 inhibitor (e.g., rimonabant), RAS signaling inhibitor (e.g., lovastatin), STEP inhibitor, S6K inhibitor, PAK inhibitor (e.g., FRAX486), MMP9 inhibitor (e.g., minocycline), and GSK3β inhibitor (e.g., lithium). In particular embodiments, treating the subject comprises providing the subject with a ketogenic (“keto”) diet.
Systems In another aspect, the present disclosure provides a system, comprising one or more polynucleotide probes and/or one or more polynucleotide primers configured to detect, in a biological sample, the level and/or splicing of the at least one biomarker associated with fragile X syndrome (FXS).
In some embodiments, the biomarker is a RNA biomarker. In certain embodiments, the at least one RNA biomarker is selected from the group consisting of AGAP1, RAB25, FAM3B, XKR3, MAP3K15, LEP, RP11-706O15.3, GCOM1, CXCL6, RGL3, NECAB2, TGM3, LRRC6, MAB21L3, RP11-36B15.1, AC091878.1, RP11-154H23.3, NOV, AC093495.4, RP11-455F5.6, RGPD2, COL9A3, CLEC18A, RP11-256L6.2, LINC01127, SLC38A11, EFCAB12, LA16c-380H5.5, CXCL1, RP11-1334A24.5, AC100793.2, ANKDD1A, AVIL, RP11-44F14.8, RP11-290F20.1, AC116366.5, EPHB4, ST6GALNAC3, PANX2, CREB5, KIAA0319, HECW2, ADCY4, LINC00173, RP11-59D5_B.2, RP11-274B18.2, RP11-213H15.3, CORO7-PAM16, HAL, DPEP3, AC002467.7, MGAM, PNMA8A, FMR1, S100B, RP11-885N19.6, RP11-545I5.3, AC091814.2, KLRC2, L1TD1, PGBD5, MXRA7, CROCC2, SEMA5A, PLA2G4C, RP11-1008C21.1, TANC1, C4orf50, NUAK1, AC104809.4, RGS17, KCNS1, DRAXIN, B3GAT1, ARHGEF28, KIF19, APOL4, GZMH, GAS1, SCD5, GLB1L2, IGHA1, KNDC1, RP11-383H13.1, FGFR2, TFCP2L1, PDGFRB, LAG3, GPR153, PODN, CKB, CERCAM, ZNF365, JUP, TRNP1, JAKMIP1, CPXM1, SLC1A7, LGR6, FCRL6, MORN4, TUBB2A, PRSS23, BFSP1, NCALD, ZNF573, PAK1, MIR4435-2HG, CD8B, PDGFC, TRAPPC2L, AC006504.5, ZNF512, FAM228B, NEIL2, FAM78A, FYB1, RNF216P1, ZCWPW1, DTX2, ATP5MD, MX2, LYRM1, GUF1, DPH7, NSFL1C, MTMR1, GTPBP10, RGS3, DRAM2, RHOH, LAIR2, GBP3, GTF2H1, XPNPEP3, ZNF888, TBC1D5, AC060780.1, SDHAP2, KMT2A, SH3BP2, CSNK1G2, NSUN5P1, LINC01128, RNF19A, SNHG8, TOP1MT, AL135818.1, CR1, CRIM1, NAP1L1, AC004593.2, SEC61A2, PCNX2, TPT1-AS1, HLA-A, LUCAT1, PTPN2, SEC31B, POLR2J3, POLR2J4, CAST, POLR2J4, NUMBL, PRMT7, ATF7IP2, TIMM23B-AGAP6, ADGRE2, GTF2H2B, MICA, SLC29A2, ZBTB10, NLGN3, METTL25, ADAM15, SSH1, SIRPB1, PARP2, PACRGL, ENTPD1-AS1, FUZ, SDR39U1, EPOR, ZSCAN26, SNHG17, GPS2, NECAP1, MRPL11, DNAJC19, ANKZF1, C1orf162, PIGT, SLC25A37, AP1G1, CIC, ITGB7, ATG16L2, BECN1, ARHGEF40, BANP, PIGA, RAD52, IRF3, CEP78, SPINT1, TMEM156, NT5C3B, PLD2, ANKRD12, CASP8, PACS2, HLA-DMA, DHPS, PDCD6, SNX5, MPPE1, AC016394.2, DPM1, E2F5, PTPN7, MTFP1, TOR1AIP1, POT1, JOSD2, NLRX1, FDXR, ZDHHC16, ALKBH4, RPS9, ZNF302, TENT4B, TKT, CARD8, RBM26, WSB1, DDX60L, ATP11A, SRGAP2, CEACAM21, COX18, WDR47, PATZ1, POLM, CC2D1B, CLK4, MIB2, PHF1, KANSL1 or TCF3, or a combination thereof.
Non-limiting examples of hybridization formats include solution phase, solid phase, and mixed phase. In some embodiments, the one or more polynucleotide probes are immobilized on a solid substrate.
In particular embodiments, the system is a microarray. Array-based detection can be performed using commercially available arrays, e.g., from Affymetrix/Thermo Fisher Scientific or other manufacturers. See, e.g., Schena et al., Science 270(5235):467-70 (1995) and Barbulovic-Nad et al., Crit Rev Biotechnol 26(4):237-59 (2006), the contents of which are incorporated herein by reference.
Primers and/or probes for detecting and/or quantifying RNA biomarkers of the disclosure can be designed using conventional methodology by those skilled in the art, for example, using custom probe designing tools available through commercial vendors.
In some embodiments, the primer is a DNA polynucleotide. In some embodiments, the primer has a length of at least about 12 nucleotides, for example, at least about: 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 nucleotides. In some embodiments, the primer has a length of about 12-40 nucleotides, for example, about: 12-35, 12-30, 12-25, 13-40, 13-35, 13-30, 13-25, 14-40, 14-35, 14-30, 14-25, 15-40, 15-35, 15-30 or 15-25 nucleotides. In certain embodiments, the primer has a length of about 15-25 nucleotides. In particular embodiments, the primer has a length of about: 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35 or 40 nucleotides. In some embodiments, the primer is an oligonucleotide.
In some embodiments, the primer is complementary to at least a portion of an RNA biomarker that has an altered (e.g., increased or reduced) expression in the biological sample, relative to a control sample. In certain embodiments, the primer is complementary to at least a portion of an exon that has an altered (e.g., increased or reduced) exon skipping in the biological sample, relative to a control sample. In particular embodiments, the primer is complementary to at least a portion of an exon that has an altered (e.g., increased or reduced) mutually exclusive exon switching in the biological sample, relative to a control sample. In some embodiments, the primer is complementary to an alternative 5′ splice site that has an altered (e.g., increased or reduced) splicing in the biological sample, relative to a control sample. In certain embodiments, the primer is complementary to an alternative 3′ splice site that has an altered (e.g., increased or reduced) splicing in the biological sample, relative to a control sample. In particular embodiments, methods of the disclosure also include using a control primer that is complementary to a sequence that is not altered in its expression and/or splicing in the biological sample, relative to a control sample.
In some embodiments, the probe is a DNA polynucleotide. In some embodiments, the probe has a length of at least about 12 nucleotides, for example, at least about: 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 nucleotides. In some embodiments, the probe has a length of about 12-40 nucleotides, for example, about: 12-35, 12-30, 12-25, 13-40, 13-35, 13-30, 13-25, 14-40, 14-35, 14-30, 14-25, 15-40, 15-35, 15-30 or 15-25 nucleotides. In certain embodiments, the probe has a length of about 15-25 nucleotides. In particular embodiments, the probe has a length of about: 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35 or 40 nucleotides. In some embodiments, the probe is an oligonucleotide.
In some embodiments, the probe is complementary to at least a portion of an RNA biomarker that has an altered (e.g., increased or reduced) expression in the biological sample, relative to a control sample. In certain embodiments, the probe is complementary to at least a portion of an exon that has an altered (e.g., increased or reduced) exon skipping in the biological sample, relative to a control sample. In particular embodiments, the probe is complementary to at least a portion of an exon that has an altered (e.g., increased or reduced) mutually exclusive exon switching in the biological sample, relative to a control sample. In some embodiments, the probe is complementary to an alternative 5′ splice site that has an altered (e.g., increased or reduced) splicing in the biological sample, relative to a control sample. In certain embodiments, the probe is complementary to an alternative 3′ splice site that has an altered (e.g., increased or reduced) splicing in the biological sample, relative to a control sample. In particular embodiments, methods of the disclosure also include using a control probe that is complementary to a sequence that is not altered in its expression and/or splicing in the biological sample, relative to a control sample.
Methods and Compositions for Stratifying Fragile X-Associated Disorder Patients In another aspect, the present disclosure provides a method of stratifying a population of subjects having, or having a propensity to develop, fragile X-associated disorder (e.g., FXS), wherein the method comprises assaying biological samples from the subjects for the presence of FMR1 RNA isoform 12.
In another aspect, the present disclosure provides a method of stratifying a set of subjects having fragile X-associated disorder (e.g., FXS), e.g., wherein the method comprises assaying FMR1 RNA in a biological sample from the subject, and stratifying the set of subjects for treatment based on the level of the FMR1 RNA in the biological sample.
In another aspect, the present disclosure provides a method for assessing the efficacy of a drug (outcome measure) for treatment of fragile X-associated disorder (e.g., FXS), comprising stratifying a population of subjects to create a stratified population comprising a subpopulation who has the FMR1 RNA isoform 12 and a subpopulation who does not have the FMR1 RNA isoform 12, and administering the drug to the subpopulation who has FMR1 RNA isoform 12, or to both subpopulations.
The FMR1 gene is located within chromosome band Xq27.3 between base pairs 147,911,919 and 147,951,125. The assembly of FMR1 gene transcript that comprises 17 exons (corresponding to the UniProtKB reference number Q06787) is known as the normal FMR1 RNA splicing. That is, the first exon (between base pairs 147,911,919 and 147,912,230, SEQ ID NO: 7) is spliced to the second exon (between base pairs 147,921,933 and 147,921,985, SEQ ID NO: 8) to produce “isoform 1” or “isol.” FMR1 isoform 1 is produced in typical developing individuals and a subpopulation of FXS subjects.
In a subpopulation of FXS subjects, the first exon (between base pairs 147,911,919 and 147,912,230, SEQ ID NO: 7) is spliced to a pseudo exon (between base pairs 147,912,728 and 147,914,451, SEQ ID NO: 9) to produce “isoform 12” or “iso12.” This predicted isoform is also annotated as FMR1-217 or ENST00000621447.1.
(SEQ ID NO: 7)
CTCAGTCAGGCGCTCAGCTCCGTTTCGGTTTCACTTCCGGTGGAG
GGCCGCCTCTGAGCGGGCGGCGGGCCGACGGCGAGCGCGGGCGGC
GGCGGTGACGGAGGCGCCGCTGCCAGGGGGCGTGCGGCAGCGCGG
CGGCGGCGGCGGCGGCGGCGGCGGCGGAGGCGGCGGCGGCGGCGG
CGGCGGCGGCGGCTGGGCCTCGAGCGCCCGCAGCCCACCTCTCGG
GGGCGGGCTCCCGGCGCTAGCAGGGCTGAAGAGAAGATGGAGGAG
CTGGTGGTGGAAGTGCGGGGCTCCAATGGCGCTTTCTACAAG
(SEQ ID NO: 8)
GCATTTGTAAAGGATGTTCATGAAGATTCAATAACAGTTGCATTT
GAAAACAA
(SEQ ID NO: 9)
CATTGGGACTTCGGAGAGCTCCACTGTTCTGGGCGAGGGCTGTGA
AGAAAGAGTAGTAAGAAGCGGTAGTCGGCACCAAATCACAATGGC
AACTGATTTTTAGTGGCTTCTCTTTGTGGATTTCGGAGGAGATTT
TAGATCCAAAAGTTTCAGGAAGACCCTAACATGGCCCAGCAGTGC
ATTGAAGAAGTTGATCATCGTGAATATTCGCGTCCCCCTTTTTGT
TAAACGGGGTAAATTCAGGAATGCACATGCTTCAGCGTCTAAAAC
CATTAGCAGCGCTGCTACTTAAAAATTGTGTGTGTGTGTTTAAGT
TTCCAAAGACCTAAATATATGCCATGAAACTTCAGGTAATTAACT
GAGAGTATATTATTACTAGGGCATTTTTTTTTTAACTGAGCGAAA
ATATTTTTGTGCCCCTAAGAACTTGACCACATTTCCTTTGAATTT
GTGGTGTTGCAGTGGACTGAATTGTTGAGGCTTTATATAGGCATT
CATGGGTTTACTGTGCTTTTTAAAGTTACACCATTGCAGATCAAC
TAACACCTTTCAGTTTTAAAAGGAAGATTTACAAATTTGATGTAG
CAGTAGTGCGTTTGTTGGTATGTAGGTGCTGTATAAATTCATCTA
TAAATTCTCATTTCCTTTTGAATGTCTATAACCTCTTTCAATAAT
ATCCCACCTTACTACAGTATTTTGGCAATAGAAGGTGCGTGTGGA
AGGAAGGCTGGAAAATAGCTATTAGCAGTGTCCAACACAATTCTT
AAATGTATTGTAGAATGGCTTGAATGTTTCAGACAGGACACGTTT
GGCTATAGGAAAATAAACAATTGACTTTATTCTGTGTTTACCAAT
TTTATGAAGACATTTGGAGATCAGTATATTTCATAAATGAGTAAA
GTATGTAAACTGTTCCATACTTTGAGCACAAAGATAAAGCCTTTT
GCTGTAAAAGGAGGCAAAAGGTAACCCCGCGTTTATGTTCTTAAC
AGTCTCATGAATATGAAATTGTTTCAGTTGACTCTGCAGTCAAAA
TTTTAATTTCATTGATTTTATTGATCCATAATTTCTTCTGGTGAG
TTTGCGTAGAATCGTTCACGGTCCTAGATTAGTGGTTTTGGTCAC
TAGATTTCTGGCACTAATAACTATAATACATATACATATATATGT
GTGAGTAACGGCTAATGGTTAGGCAAGATTTTGATTGACCTGTGA
TATAAACTTAGATTGGATGCCACTAAAGTTTGCTTATCACAGAGG
GCAAGTAGCACATTATGGCCTTGAAGTACTTATTGTTCTCTTCCA
GCAACTTATGATTTGCTCCAGTGATTTTGCTTGCACACTGACTGG
AATATAAGAAATGCCTTCTATTTTTGCTATTAATTCCCTCCTTTT
TTGTTTTGTTTTGTAACGAAGTTGTTTAACTTGAAGGTGAATGAA
GAATAGGTTGGTTGCCCCTTAGTTCCCTGAGGAGAAATGTTAATA
CTTGAACAAGTGTGTGTCAGACAAATTGCTGTTATGTTTATTTAA
TTAAGTTTGATTTCTAAGAAAATCTCAAATGGTCTGCACTGATGG
AAGAACAGTTTCTGTAACAAAAAAGCTTGAAATTTTTATATGACT
TATAATACTGCTGTGAGTTTTAAAAGTAAAGCAAAAGTAAACTGA
GTTGCTTGTCCAGTGGGATGGACAGGAAAGATGTGAAATAAAAAC
CAATGAAAAATGAA
Additional information on Exon 1, the pseudo exon, and isoform 12 can be found at: useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;g=ENSG00000102081;r=X :147911951-147951125;t=ENST00000370475; and useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;g=ENSG00000102081;r=X :147911951-147951125;t=ENST00000621447, the contents of both of which are incorporated herein by reference in their entirety.
In some embodiments, the presence of FMR1 RNA isoform 12 in the biological sample is assayed before, during, and/or after a therapeutic treatment for evaluating therapeutic efficacy (outcome measure).
The subject can be any one of the subjects disclosed herein.
EXEMPLIFICATION Most FXS studies focus on Fmr1 knockout (KO) mouse models. Shah et al. show, for the first time, that Fmr1 KO mice have dysregulated pre-mRNA splicing in the hippocampus part of the brain (Shah et al., Cell Rep. 30(13):4459-72 (2020)). The present disclosure shows that missplicing in the Fmr1 KO mouse occurs in all brain regions tested, as well as all peripheral tissues tested. Because FMRP is likely present in all cells, missplicing probably also occurs in all cells.
Based on the mouse FMRP knockout data, it is surmised that RNA missplicing would also occur in human cells, and possibly white blood cells (WBCs) (red blood cells and platelets are anucleate). It is believed that RNA biomarkers from biological samples comprising such cells would be more easily obtainable than biomarkers from brain tissues, and can be used for FXS diagnosis, prognosis, and patient stratification. The methods disclosed herein would be a useful platform for testing drug efficacy and perhaps stratification of individuals (e.g., individuals with FXS), and would be useful for personalized medicine for individuals with FXS.
Example 1. Methods Human FXS Participant Studies All samples collected for the study were based on voluntary informed consent provided by the participants in accordance with Rush University Medical Center IRB regulations. All participants were Caucasian males with a FMR1 full mutation (CGG repeats >200) or typically developing individuals (CGG repeats <55) as confirmed by DNA analysis. Intelligence quotient (IQ) scores were obtained using the Stanford-Binet Scale—Fifth Edition (SB5) (Roid and Pomplun, 2012). The adaptive skills of participants was determined using an semi-structured interview and measured using the Vineland Adaptive Behavior skills (Vineland-3). The Adaptive Behavior Composite (ABC) standard score (SS) is the measure of overall adaptive functioning based on scores assessing the following domains: communication, daily living skills, and socialization. All FXS males in the study were diagnosed with Autism Spectrum Disorders (ASD) based on both Autism Diagnostic Observation Schedule (ADOS) assessments and the Diagnostic and Statistical Manual-5th Edition criteria (DSM-5) (ref) by clinicians with expertise in idiopathic ASD, and ASD in FXS. FXS patients were aged 16-38 years with FXS phenotypes, an IQ range of 20-52 and ABC standard score range of 20-41 (Table 1). Age matched TD individuals for the study were aged 22-29 with a normal IQ and no known neuropsychiatric conditions (Table 1).
For CGG repeat size determination in the 5′ UTR of the FMR1 gene, DNA isolated from whole blood was analyzed using the Asuragen FMR1 Amplidex PCR Kit. Methylation status was determined using the Asuragen FMR1 methylation PCR Kit and/or Southern blot analysis. FMRP levels were quantified by generating dried blood spots (DBS) from the samples. FMRP levels were quantified by generating dried blood spots (DBS) from the samples. To generate DBS, 12-50 μl spots were put on each blood card and allowed to dry. The blood cards were then stored at−80. Discs were punched using a 6 mm punch and incubated in lysis buffer. Extracted sample was centrifuged and FMRP quantified using the Luminex Microplex immunochemistry assay. FMRP levels were normalized to 1000 WBCs per sample. Additionally, FMRP levels were also quantified by using peripheral blood mononuclear cells (PBMC) samples. PBMC were isolated from whole blood using a Cell Preparation (CPT) blood tubes. Isolated PBMC were lysed and quantified for total protein concentration using a spectrophotometer and FMRP quantified using a Luminex Microplex immunochemistry assay. FMRP levels were normalized to total protein. Both methods produced comparable levels of FMRP in the samples assessed.
Frozen post-mortem brain tissues were obtained from University of California at Davis Brain Repository from FXS male individuals (N=6) and age-matched typically developing (TD) males (N=5).
RNA Extraction and Sequencing RNA was extracted from patient leukocytes using the LeukoLOCK™ total RNA isolation system (AM1923, Thermo Fisher Scientific, Waltham, MA). Ten mL fresh blood was collected from FXS male patients (N=10) and age-matched typically developing males (N=7) (controls) in an anti-coagulant containing tube, and RNA was extracted using a LeukoLOCK™ fractionation & stabilization kit (AM1933, Thermo Fisher Scientific, Waltham, MA), per the manufacturer's instructions. Briefly, the blood sample was passed through a LeukoLOCK™ filter and 3 mL phosphate buffered saline (PBS) was used to rinse the filter followed by 3 mL of RNAlater® RNA Stabilization Solution (Thermo Fisher Scientific, Waltham, MA). The residual RNAlater® was expelled from the LeukoLOCK™ filter and the filters were capped and stored at −80° C.
To extract RNA, the filters were thawed at room temperature for 5 mins and then the remaining RNAlater® was removed. The filter was flushed with 4 ml of TRI Reagent, and the lysate was collected in a 15-ml tube. 800 μl 1-Bromo-3-chloropropane (BCP) was added to each tube and vortexed vigorously for 30 seconds. The tube was then incubated at room temperature for 5 minutes. After centrifugation for 10 minutes at 4° C. at ˜2,000×g, the aqueous phase was recovered. To recover long RNA fractions, 0.5 volumes of 100% ethanol were added and mixed well. The RNA was then recovered using the RNA clean and concentrator kit. DNase treatment was performed using Turbo™ DNase (Thermo Fisher Scientific, Waltham, MA), and the RNA obtained was resuspended in RNAse free water and stored at −80° C. 1 μg of the RNA was used for cDNA synthesis using the QuantiTect® reverse transcription kit (Qiagen, Hilden, Germany) to assess for depletion of the Globin mRNA using qPCR, to confirm exclusion of red blood cells from the prep. 3 μg of RNA sample was sent to Novogene (Beijing, China) for a directional mRNA library preparation using polyA enrichment. The libraries were sequenced on the NovaSeq platform to generate paired end, 150 bp reads.
The post-mortem frozen cortical tissues from FXS male individuals (N=6) and age-matched typically developing (TD) males (N=5), were powdered in liquid nitrogen using a mortar and pestle. The fine powder was then homogenized on ice in a dounce homogenizer using TRIzol™ Reagent (ThermoFisher Scientific #15596026) and the lysate collected. Total RNA was extracted using BCP and recovered as above and stored at −80° C.
Brain Tissue The post-mortem frozen cortical tissues from FXS male individuals (N=6) and age-matched typically developing (TD) males (N=5) were powdered in liquid nitrogen using a mortar and pestle. The fine powder was then homogenized on ice in a Dounce homogenizer using TRIzol™ Reagent (ThermoFisher Scientific #15596026), and the lysates were collected. Total RNA was extracted using BCP, recovered as described above, and stored at −80° C.
cDNA Synthesis and qPCR
One μg of total RNA was primed with oligo(dT)20 to generate cDNA with a QuantiTect cDNA synthesis kit (Qiagen, #205311) using random hexamers. qPCR was performed using the iTaq™ Universal SYBR® Green Supermix (BIO-RAD #1725122) on a QuantStudio 3 qPCR machine in duplicate.
RNA-Seq Data Analysis Fastq files were uploaded to the DolphinNext platform (Yukselen et al., BMC Genomics 21(1):310 (2020)) at the UMMS Bioinformatics Core for mapping and quantification. The reads were subjected to FastQC (v0.11.8) analysis, and the quality of reads was assessed. 9-nt molecular labels were trimmed from both 5′ ends of the pair-end reads and quality-filtered with Trimmomatic (0.32). Reads mapped to human rRNA by Bowtie2 (2.1.0) were filtered out. Cleaned reads were next mapped to the Refseq (V38) human transcriptome and quantified by RSEM (1.2.11). Gene Ontology (GO) enrichment analysis was done using the clusterProfiler package (Yu et al., 2012) for biological processes enriched in the differentially expressed genes. Estimated counts on each gene were used for the differential gene expression analysis by DESeq2 (1.16.1). After the normalization by median of ratios method, only the genes with minimal 5 counts average across all samples were kept for the Differential Gene expression analysis. The FDR (padj) cut-off <5% was used. The TDF files generated were uploaded on the Integrative Genomics Viewer for visualization.
The ratio between reads including or excluding exons, also known as “Percent Spliced In” (PSI), indicates how efficiently sequences of interest are spliced into transcripts. The False Discovery Rate (FDR) is a method of conceptualizing the rate of type I errors in null hypothesis testing when conducting multiple comparisons.
Alternative Splicing Analysis RNA-seq data generated from leukocytes from FXS male patients (N=10) and age-matched typically developing males (N=7) was used to analyze alternative splicing (AS) using the rMATS package v3.2.5 (Shen et al., Proc Natl Acad Sci USA. 111(51):E5593-601 (2014)) with default parameters. The Percent Spliced In (PSI) levels or the exon inclusion levels were calculated by rMATS using a hierarchical framework. To calculate the difference in PSI between genotypes, a likelihood-ratio test was used. AS events with an FDR<5% and |deltaPSI|≥5% as identified using rMATS were used for further analysis.
Primers Sets for Detecting FMR1 Isoforms Iso12_1Forward:
(SEQ ID NO: 1)
5′ AGAAGATGGAGGAGCTGGTG 3′
Iso12_1Reverse:
(SEQ ID NO: 2)
5′ CAGTGGAGCTCTCCGAAGTC 3′
Iso12_2Forward:
(SEQ ID NO: 3)
5′ CCAGCAGTGCATTGAAGAAG 3′
Iso12_2Reverse:
(SEQ ID NO: 4)
5′ CTGAAGCATGTGCATTCCTG 3′
Iso1_1 Forward:
(SEQ ID NO: 5)
5′ AGAAGATGGAGGAGCTGGTG 3′
Iso1_1 Reverse:
(SEQ ID NO: 6)
5′ TTCATGAACATCCTTTACAAAT
GC 3′
Differential gene expression analysis: DESeq2 (v3.9) was used to obtain differentially expressed genes from the estimated counts table. After normalization by the median of ratios method, genes with minimal 5 counts average across all samples were kept for the Differential Gene expression analysis. The Padj<5% was used as a cutoff. The TDF files generated were uploaded on the Integrative Genomics Viewer (2.6.2) for visualization.
Alternative splicing analysis: To analyze differential alternative splicing (AS), the rMATS package v3.2.5 (Shen et al., 2014) was used with default parameters. The Percent Spliced In (PSI) levels or the exon inclusion levels calculated by rMATS using a hierarchical framework. To calculate the difference in PSI between genotypes a likelihood-ratio test was used. AS events with an FDR<5% and |deltaPSI|≥5% as identified using rMATS were used for further analysis The genes with significant skipped exons were used for validation using RT-qPCR analysis. One ug of RNA was used to generate cDNA using the QuantiTect cDNA synthesis kit. Primers were designed to overlap skipped/inclusion exon junctions and qPCR was performed using the Bio-Rad SYBR reagent on a Quantstudio3 instrument.
Alternative polyadenylation (APA) analysis: Differential polyadenylation site usage was assessed using the APAlyzer (Wang and Tian, 2020). The RNA-seq read density between the last exon and the proximal (Sh-Short) polyadenylation site and for the distal (Ln-long) polyadenylation site was calculated, which determine the constitutive (cUTR) and the alternative (aUTR) 3′UTR, respectively. The difference in APA for a gene is calculated using a Relative-Expression(RE) score−log 2(RDaUTR/RDcUTR). The RE difference and the P value<0.05 was used to determine 3′UTR lengthening ‘UP’ and 3′UTR shortening; ‘DN’. ‘NC’ indicates no significant change. To assess intronic polyadenylation (IPA), the read density upstream and downstream of the intronic polyadenylation site was calculated and genes with activation or use of the IPA site are indicated by ‘UP’ and suppression of the IPA site use between the genotypes is indicated by ‘DN’. ‘NC’ indicates no significant change. Average reads count >5 in each replicate in each region (aUTR and cUTR) were used as a cutoff.
Chromatin Immunoprecipitation Sequencing (ChIP-Seq) Eight mL fresh blood was collected from FXS male (N=10) and age-matched typically developing males (N=7) individuals (See Supplemental Table 1) in a BD vacutainer CPT (Cell Preparation Tube with sodium citrate-blue top tube, Becton Dickinson #REF362761). The tube was gently inverted 5 times and the sample was centrifuged for 25 minutes at 1500-1800 RCF at room temperature. The tubes were then inverted to collect the lymphocytes and other mononuclear cells resuspended in the upper liquid phase in a new 15 mL tube. The samples were centrifuged again for 10 minutes at 300 RCF to obtain the PBMC (peripheral blood mononuclear cells) pellet. The PBMCs were rinsed with 1× Dublecco's phosphate buffered saline w/o calcium or magnesium (D-PBS) (Invitrogen #14190-094). The PBMC pellet was resuspended in 250 uL ice-cold D-PBS with protease inhibitors. Chromatin isolation and sequencing was performed as previously described (Shah et al., 2020). Briefly the cells were cross-linked with 1% formaldehyde and quenched with 150 mM glycine. After centrifugation at 2000 g for 10 min at 4° C. the cells were lysed. After homogenization the nuclei were harvested by centrifugation at 2000 g for 5 min at 40 C The nuclei were lysed by incubating for 20 mins on ice in nuclear lysis buffer (10 mM Tris (pH 8.0), 1 mM EDTA, 0.5 mM EGTA). 0.5% SDS was added and the samples sonicated on a Bioruptor® sonicator at high power settings for 9 cycles (sonication: 30 sec on, 90 sec off) of 15 min each at 4° C. The samples were centrifuged and diluted to adjust the SDS concentration to <0.1%. 10% of each sample was used as input. The remainder of the samples were divided into two and incubated with protein G dynabeads coupled overnight at 40 C with antibodies against H3K36me3 (Abcam ab9050, 5 μg per ChIP) or H3K4me3 (Active Motif-39159, 5 g per ChIP). After IP, the beads were washed and chromatin and de-crosslinked overnight at 65° C. After RNAse and proteinase K treatment the DNA was purified. ChIP-Seq libraries were prepared by performing the following steps: ends repair using T4 DNA polymerase, A′ base addition by Klenow polymerase and Illumina adapter ligation using T4 Polynucleotide kinase from New England Biolabs (NEB). The library was PCR amplified using multiplexing barcoded primers. The libraries were pooled with equal molar ratios, denatured, diluted, and sequenced with NextSeq 500/550 High Output Kit v2.5 (Illumina, 75 bp paired-end runs) on a Nextseq500 sequencer (Illumina).
ChIP-Seq Analysis For ChIP-seq data analysis, alignments were performed with Bowtie2 (2.1.0) using the GRCh38 (hg38) version 34 genome, duplicates were removed with Picard and TDF files for IGV viewing were generated using a ChIP-seq pipeline from DolphinNext (Yukselen et al., 2019). The broad peaks for H3K36me3 ChIP-Seq were called using the broad peak parameter MACS2. Narrow peaks for H3K4me3 ChIP were called using the narrow parameter in MACS2. deepTools (Ramirez et al., 2016) was used to plot heatmaps and profiles for genic distribution of H3K36me3 and H3K4me3 ChIP signals over input. IGV tools (2.6.2) were used for visualizing TDF files and all tracks shown were normalized for total read coverage.
Cell Culture Lymphoblast Cell Lines Lymphoblast cell lines (LCL) were obtained from Coriell Institute from two FXS individuals (GM07365 (FXS1), GM06897 (FXS2)) and two typically developing control males (GM07174 (WT3), GM06890 (WT4)). Cells were cultured in RPMI 1640 medium (Sigma-Aldrich), supplemented with 15% fetal bovine serum (FBS) and 2.5% L-glutamine at 37° C. with 5% CO2 in T25 flasks.
Fibroblast Cells Skin biopsies from participants were collected in a 15 cc tube with transfer culture media (DMEM with 5% Gentamicin). The biopsy was then removed from the transfer media with tweezers onto a sterile tissue culture dish and dissected into approximately 6-7 pieces using sterile tweezers and scissors in the culture hood. Three to four pieces of skin explants were kept on the bottom of a T25 flask and 3 ml CHANG AMNIO culture media was added. The flask was then incubated at 37° C. with 5% CO2 for 10 days. The culture media was changed after cells started growing out from the skin explants. After the cells had grown to 5-6 layers around the skin explants, the skin explants were removed from the culture flask and fibroblasts were trypsinized and spread evenly in the flask. The media were changed after overnight incubation with trypsin. Fibroblast culture medium was added (complete media-(500 ml DMEM (15-017-CV) with 10% FBS and 1× antibiotic-antimitotic, 1×L-glutamine 5 ml)) twice a week to cells in a T25 culture flasks at 37° C. with 5% CO2.
5-AzadC Treatment For each cell culture, 30×105 cells/ml were added to a final volume of 20 ml media (RPMI1640 medium (Sigma-Aldrich) supplemented with 15% fetal bovine serum (FBS) and 2.5% L-glutamine at 37° C. with 5% C02) per T25 flask. 5-Aza-2′-deoxycytidine (5-AzadC) (Sigma-Aldrich, A3656) was added to the cell cultures (final concentration 1 μM) for 7 consecutive days. A 2 mM stock of 5-AzadC was made in DMSO. For each cell line, two independent treatments were performed (n=2). For the no treatment controls for each cell line, DMSO was added to the flasks. For samples with both 5-AzadC and ASO treatment, 80 nM or 160 nM ASOs or vehicle were added on Day 1 and either 5-AzadC or DMSO was added each day from Day 2 up to Day 9 at a final concentration of 1 μM. On Day 9 the cells were collected in 1× phosphate buffered saline to proceed with RNA extraction or Western blotting.
Western Blotting Cells were homogenized at 4° C. in RIPA buffer, with incubation on ice for 10 minutes and dissociation by pipetting. The extract was centrifuged at 13,200 rpm for 10 minutes at 4° C., and the supernatant collected. Protein concentration was determined using BCA reagent. Proteins (10 g) were diluted in SDS-bromophenol blue reducing buffer with 40 mM DTT and analyzed using western blotting with the following antibodies: FMRP (Millipore, mAb2160, 1:1,000), FMRP (Abcam, ab17722, 1:1,000) and GAPDH (14C10, Cell Signaling Technology, mAb 2118, 1:2,000), diluted in 1× TBST with 5% non-fat milk. Membranes were washed three times for 10 minutes with 1×TBST and incubated with anti-rabbit or anti-mouse secondary antibodies (Jackson, 1:10,000) at room temperature for 1 hour. Membranes were washed three times for 10 minutes with 1×TBST, developed with ECL-Plus (Piece), and scanned with GE Amersham Imager.
Quantification and Statistical Analysis All grouped data are presented as mean±s.e.m. All tests used to compare the samples are mentioned in the respective figure. legends and corresponding text. When exact P values are not indicated, they are represented as follows: *, p<0.05; **, p<0.01; ***, p<0.001; ****, P value<0.0001; n.s., p>0.05.
Example 2. Gene Expression Changes in Leukocytes from FXS Individuals To investigate whether mis-splicing of mRNAs also occurs in blood samples from individuals with Fragile X Syndrome (FXS), deep (60-90 million reads) and long read (150PE) RNA-seq on freshly obtained leukocytes from 29 FXS males and 13 age-matched typically developing (TD) males was performed. CGG repeat expansion (>200) for all samples and FMR1 promoter methylation status for FXS samples when available was confirmed by either southern blot or methylation PCR assays.
Differential gene expression (DGE) and differential alternative splicing (DAS) were conducted. DGE analysis revealed that ˜50 RNAs were up- or down-regulated in FXS leukocytes relative to TD (P value<0.0002) (FIG. 1) and were clustered based on their z-scores (FIG. 2). FXS individuals are indicated with black squares, while TD individuals are indicated with white squares.
S100B (S100 calcium-binding protein B), AGAP1 (ArfGAP With GTPase Domain, Ankyrin Repeat And PH Domain 1), FAM3B (FAM3 Metabolism Regulating Signaling Molecule B), and RAB25 (RAS oncogene family member 25) are examples of RNAs that were depleted or up-regulated in the FXS samples relative to TD (log 2FC, P value<0.0002) (FIG. 3). The differential expression of these RNAs in FXS leukocytes was confirmed by RT-qPCR (FIG. 4). The decreased levels of S100B and increase in RAB25 levels in FXS cells were also confirmed in a lymphoblastoid cell line from a FXS individual (FXS2, GM06897, Coriell Institute) using qPCR assays (FIG. 5).
Finally, differential splicing using rMATS was assessed, finding hundreds of statistically significant events that were altered between genotypes (FXS vs. TD) (using an FDR<5% and a difference in the exon inclusion levels (PSI, Percent spliced-in) between the genotypes (deltaPSI) of ≥5% (FIG. 6A). A violin plot of the DAS demonstrates that most significant splicing changes were −/+˜10% in FXS vs TD with some changes near 30-40% (FIG. 6B). Using RT-PCR the increased skipping of exon 3 in the LAIR2 (leukocyte associated immunoglobulin like receptor 2) RNA was confirmed, which shows ˜20% increased skipping in FXS samples in the DAS analysis (FIGS. 7A and 7B).
A previous study showed that Fmr1-dependent changes in the epigenetic mark H3K36me3 (histone H3 trimethylation at lysine 36) were correlated with aberrant alternative splicing in mouse hippocampus (Shah et al., Cell Rep. 30(13):4459-72 (2020)). Fmr1-dependent changes in RNA levels were also correlated with the chromatin mark H3K4me3 (histone H3 trimethylation at lysine 4) in cultured mouse neurons. Consequently, ChIP-Seq was performed to determine whether similar changes in chromatin marks occur in FXS cells. However, results from FXS (n=2) and TD (n=3) leukocyte samples showed no genotype-specific changes in H3K36me3 or H3K4me3 (FIG. 10 and FIG. 11).
Example 3. FXS-Specific RNA Biomarkers White blood cells were isolated from freshly drawn blood from 10 FXS individuals (males, ˜12-38 yrs) and 7 age-matched typically developing individuals (males, “TD” or “control”). RNA was extracted from the white blood cells, and deep, paired-end large-read length sequencing and analysis were performed. Greater than 1,000 misregulated RNA “events,” all having statistical significance (p<0.05), were detected in the FXS samples relative to the control samples.
428 RNA markers were upregulated in the white blood cells of the FXS individuals compared to the typically developing individuals (FIG. 8, “x”). A genome browser view shows that the PNMA8A RNA is strongly expressed in FXS individuals but virtually absent in all typically developing individuals (FIG. 14). Non-limiting examples of RNA markers with increased expression in FXS individuals, relative to typically developing individuals, are listed in Table 1.
305 RNA markers were down regulated in the white blood cells of FXS individuals compared to typically developing individuals (FIG. 8, “Δ”). A genome browser view shows that expression of the S100B RNA is reduced in the FXS individuals, compared to typically developing individuals (FIG. 16). Non-limiting examples of RNA markers with reduced expression in FXS individuals, relative to typically developing individuals, are listed in Table 2.
GO (Gene ontology) analysis indicates that RNAs enriched in the FXS samples encode proteins involved in biological processes such as neutrophil activation and immunity-related functions while the RNAs depleted in FXS encode proteins involved T cell and natural killer cell function (FIG. 19). We next assessed differential splicing using rMATS (Shen et al., 2014) and find hundreds of statistically significant events that are altered between genotypes (FXS vs. TD) (using an FDR<5% and a difference in the exon inclusion levels (PSI, Percent spliced-in) between the genotypes (deltaPSI) of ≥5% and read count >1 in each sample) (FIG. 20).
To determine whether alternative splicing or RNA level changes in FXS leukocytes correlate with FXS-dependent alterations in H3K36me3 or H3K4me3, ChIP-seq was performed for chromatin marks. FIGS. 10 and 11 demonstrate that the distribution and levels of these marks were similar in FXS (n=2) and TD (n=3) leukocytes. These results suggest that leukocytes from FXS individuals do not regulate histone modifications in a manner similar to Fmr1-deficient mouse brain or neurons. Finally, genotype-specific changes in the usage of distal or proximal polyadenylation sites were detected in RNA 3′UTRs (FIG. 12) as well as usage of intronic polyadenylation sites (FIG. 13), which add to the repertoire of altered RNA processing events that depend on FMR1.
Most missplicing events were exon skipping or mutually exclusive exon switching. 705 RNA markers had increased exon skipping in the white blood cells of the FXS individuals, relative to the typically developing individuals (FIG. 17, “x”, less inclusion of skipped exon). Non-limiting examples of RNA markers with increased exon skipping in FXS individuals, relative to typically developing individuals, are listed in Table 4. All data are statistically significant (p<0.05 and FDR<0.05).
419 RNAs had reduced exon skipping in the white blood cells of the FXS individuals, relative to the typically developing individuals (FIG. 17, “▴”, more inclusion of skipped exon). Non-limiting examples of RNA markers with reduced exon skipping in FXS individuals, relative to typically developing individuals, are listed in Table 3. All data are statistically significant (p<0.05 and FDR<0.05).
A similar pattern occurs with mutually exclusive exon switching. 571 RNAs had increased mutually exclusive exon switching in the white blood cells of the FXS individuals, relative to the typically developing individuals (FIG. 18, “▴”, more inclusion of mutually excluded exon). Non-limiting examples of RNA markers with increased mutually exclusive exon switching in FXS individuals, relative to typically developing individuals, are listed in Table 6. All data are statistically significant (p<0.05 and FDR<0.05).
689 RNAs had reduced mutually exclusive exon switching in the white blood cells of the FXS individuals, relative to the typically developing individuals (FIG. 18, “x”, less inclusion of mutually excluded exon). Non-limiting examples of RNA markers with reduced mutually exclusive exon switching in FXS individuals, relative to typically developing individuals, are listed in Table 5. All data are statistically significant (p<0.05 and FDR<0.05).
Some RNA markers showed altered 5′ or 3′ splice sites. The top 25 RNA markers with increased alternative 5′ splice site (ASSS) in FXS individuals, relative to typically developing individuals, are listed in Table 8. Non-limiting examples of RNA markers with reduced alternative 5′ splice site in FXS individuals, relative to typically developing individuals, are listed in Table 7. Non-limiting examples of RNA markers with increased alternative 3′ splice site (A3SS) in FXS individuals, relative to typically developing individuals, are listed in Table 10. Non-limiting examples of RNA markers with reduced alternative 3′ splice site in FXS individuals, relative to typically developing individuals, are listed in Table 9. All data are statistically significant (p<0.05 and FDR<0.05).
These findings suggest that RNA markers can be used for diagnosing an individual as having FXS, or having a propensity to develop FXS.
Example 4. FMR1 Isoform 12 Detected in a Subpopulation of FXS Patients Expansion of >200 CGG repeats in FMR1 induces gene methylation, transcriptional silencing, loss of FMRP, and FXS. It was therefore surprising that in leukocytes of 21 of 29 FXS individuals, FMR1 RNA was detected, and in four individuals, the level of all isoforms of this RNA were similar to or even higher than those in the TD individuals (FIG. 21, FMR1 RNA TPM levels). When only full-length FMR1 encoding 632 amino acid FMRP (FMR1-205) was examined (FIG. 24), WBCs from 6 individuals had levels of this transcript that were similar to those of TD (FIG. 21). For comparison, the levels of the FMR1 paralog FXR2 were similar in all individuals (FIG. 21). Visualizing the RNA reads at the FMR1 locus with the Integrated Genome Viewer (IGV) make it evident that exonic reads were detected at robust levels in TD individuals (top 13 reads) and that the exonic reads were also detected in FXS individuals (bottom 29 reads) (FIGS. 22 and 23). FXS individuals 1-18 expressed relatively high FMR1 levels (with a cutoff of 0.6 TPM) (H FMR1) compared to FXS individuals 19-29 who expressed low or undetectable FMR1 levels (L FMR1) (FIGS. 22, 23, and 24). Remarkably, the H-FMR1 FXS individuals displayed strong RNA reads in intron 1 of FMR1 (black box FIG. 22, enlarged in FIG. 23). Notably, RNA reads in this intronic region were not detected in any TD individuals even though FMR1 RNA was strongly expressed (FIGS. 22 and 23).
The FMR1 locus expresses multiple alternatively spliced RNA isoforms (FIG. 24). The RNA reads detected in FMR1 intron 1 correspond to the second exon of the FMR1-217 RNA isoform (FIG. 24, grey box). FMR1-217 (ENST00000621447.1) is a 1.8 kb transcript comprised of two exons and is predicted to encode a 3 kDa truncated protein. RT-PCR was used to detect the FMR1-217 isoform in the FXS leukocyte samples (reverse transcription primed with oligodT(20)) and sequenced the amplified product using primers specific to the FMR1-217 exon-exon junction. Aligning this sequence to FMR1 showed that it is a spliced product of FMR1 exon one and FMR1-217 exon 2 (FIG. 24).
(SEQ ID NO: 10)
MEELVVEVRGSNGAFYKHWDFGELHCSGRGL
A scatter plot shows that overall splicing was differentially regulated in FXS individuals who expressed FMR1 RNA isoform 12, versus those who did not (FIGS. 28A-28B). 628 RNA markers had reduced exon skipping in the white blood cells of FXS individuals who expressed FMR1 RNA isoform 12 relative to those who did not (FIG. 28A, “▴”). 553 RNA markers had increased exon skipping in the white blood cells of FXS individuals who expressed FMR1 RNA isoform 12 relative to those who did not (FIG. 28A, ccx).
607 RNA markers had increased mutually exclusive exon switching in the white blood cells of FXS individuals who expressed FMR1 RNA isoform 12 relative to those who did not (FIG. 28B, “▴”). 621 RNA markers had reduced mutually exclusive exon switching in the white blood cells of FXS individuals who expressed FMR1 RNA isoform 12 relative to those who did not (FIG. 28B, “x”).
These findings suggest that RNA markers such as FMR1 RNA not only can be used for diagnosing an individual as having FXS, or having a propensity to develop FXS, but also can be used for stratifying FXS individuals. The identification FMR1 RNA isoform 12 enables stratification of FXS individuals into two subpopulations, those who express isoform 12 and those who do not. FXS individuals expressing some FMR1 RNA differ in their overall cellular splicing pattern compared to FXS individuals who do not express FMR1 RNA, thus, providing a robust basis for distinguishing the two subpopulations of FXS individuals via splicing data.
Next, the proportion of full-length FMR1 RNA to FMR1-217 RNA in TD or FXS leukocytes was assessed. In the TD samples, 95% of the total FMR1 RNA (primers Ex1F and Ex1R) represented full-length molecules (primers Ex1F and Ex2R), whereas in the H FMR1 samples, 75% of the total FMR1 RNA was full-length and 25% was FMR1-217 (primers Ex1F and 217R) (FIG. 26). In the L FMR1 samples, both isoforms were just barely detected. The total FMR1 RNA levels in all the samples were normalized to GAPDH RNA expression (* denotes P values<0.05). Importantly, all FXS individuals in this study, irrespective of FMR1 expression, displayed typical FXS symptoms, suggesting that even in patients with high FMR1 expression, functional FMRP may not be present or is present at very low amounts (FMRP protein levels were quantified for available samples (data not shown)).
Whether stratification of FXS individuals, based on relatively high (H) or low (L) amounts of FMR1 (using a cutoff of 0.6 TPM), was reflected in transcriptome-wide RNA changes was examined. By reanalyzing FXS leukocyte RNA-seq data to compare significant RNA alterations between these two groups, hundreds of aberrant splicing events that tracked with the amount of this mis-spliced transcript were found (FIG. 29 and data not shown). Whether the parameters measured in WBCs correlated with IQ was investigated. Table 11 presents determinations of methylation status of the FMR1 gene (by PCR), FMRP levels (ng/μg protein), CGG repeat number, FMR1-217, full-length FMR1-205, all detected FMR1 isoforms, and IQ (Stanford-Binet test).
TABLE 11
Characterizing Leukocytes of Each FXS Individual
PBMC [ng
CGG FMRP/μg
repeat Methylation total FMR1 FMR1-205 FMR1-217
Lab ID number (MPCR) protein] IQ (TPM)
FXS01 140, 140 100%, 175 6.56E−03 37.8 36.2 3.2 18.6
175, >200 97%, >200 90%
FXS02 >200 81% 2.07E−03 26.8 32.6 1.7 24.4
FXS03 150, >200 N/A N/A 52.0 28.5 2.0 10.6
FXS04 102, >200 N/A N/A 37.0 17.0 0.8 2.7
FXS05 >200 >200 96% 4.85E−04 35.1 10.9 0.0 10.5
FXS06 65, >200 65 98%, >200 100% 1.77E−02 55.0 8.4 0.5 0.2
FXS07 >200 N/A 2.28E−04 25.0 8.0 0.4 5.9
FXS08 173, >200 N/A N/A 39.9 4.9 0.0 2.9
(~710, ~613)
FXS09 >200 100% 4.40E−04 35.0 4.2 0.0 2.8
FXS10 >200 100% 3.11E−04 56.0 3.8 0.0 2.7
FXS11 >200 100% 6.50E−03 62.3 3.8 0.0 0.1
FXS12 >200 100% 4.85E−04 26.9 2.9 0.1 2.3
FXS13 102, 102, 174 5.35E−04 27.6 2.9 0.0 0.6
174, >200 100%, >200 100%
FXS14 >200 N/A N/A 20.0 2.2 0.2 1.3
FXS15 >200 100% 2.56E−04 45.9 2.1 0.1 1.5
FXS16 63, >200 63.98%, 194 3.50E−03 53.5 2.0 0.0 0.9
36%, >200 100%
FXS17 >200 100% 1.05E−04 44.0 1.6 0.0 1.1
FXS18 >200 N/A 1.34E−04 30.3 1.1 0.0 0.8
FXS19 >200 N/A N/A 50.0 1.0 0.0 0.7
FXS20 >200 100% 4.85E−04 29.6 0.6 0.0 0.4
FXS21 >200 100% 2.00E−04 37.7 0.6 0.2 0.3
FXS22 >200 N/A 4.88E−04 35.8 0.0 0.0 0.0
FXS23 >200 94% N/A N/A 0.0 0.0 0.0
FXS24 28**, >200 100% N/A 37.6 0.0 0.0 0.0
FXS25 >200 100% N/A N/A 0.0 0.0 0.0
FXS26 >200 100% 4.85E−04 41.8 0.0 0.0 0.0
FXS27 >200 >200 100% 4.85E−04 20.2 0.0 0.0 0.0
FXS28 >200 N/A N/A N/A 0.0 0.0 0.0
FXS29 >200 >200: 85% N/A 49 0 0 0
In Table 11, FMR1 gene methylation (MPCR): in percent as determined by PCR analysis; FMRP levels: ng/μg total protein; FMR1: all isoforms; IQ: Stanford-Binet; N/A: not available.
Table 12 presents correlation coefficients for pairwise comparisons of the measurements noted above. Methylation of the FMR1 gene is negatively correlated with FMR1-217 and FMR1-205 expression. More intriguing is the moderately positive correlation of IQ with FMRP protein levels. Somewhat surprisingly, FMR1-205, which encodes full-length FMRP, has no correlation with IQ. However, it is noted that while FMR1-205 encodes the complete 632-amino acid FMRP, other FMR1 isoforms, which vary in abundance, encode truncated FMRP proteins. Without presupposing functionality of truncated FMRP proteins, the canonical FMR1 isoform, FMR1-205, was used for further comparisons. FMR1-217 has a negative correlation with IQ, indicating a deleterious effect of this isoform. FIG. 44 displays a 3-dimensional comparison of all the parameters noted above. The inset shows that some FXS patients with a fully methylated FMR1 gene express FMR1 RNA and FMRP. Taken together, these results show several important findings. First, the FMR1 locus is frequently transcribed even when the FMR1 gene with a full CGG expansion is fully methylated. Second, FMRP levels in WBCs are positively correlated with IQ. Third, the negative correlation of FMR1-217 with IQ suggests that the process of mis-splicing, the 31-amino acid polypeptide derived from FMR1-217, and/or the FMR1-217 RNA itself (e.g., all three) might impart some toxic effect manifest in the brain (e.g., IQ). In any event, the levels of FMR1-217 expression, as well as additional transcriptome-wide changes in RNA processing events, may form the basis for molecular stratification of FXS individuals.
TABLE 12
Correlation coefficients for pairwise
comparisons for indicated parameters
FMR1- FMR1-
Methylation FMRP IQ FMR1 205 217
Methylation 1.0 −0.2 0.3 −0.9 −0.8 −1.0
FMRP −0.2 1.0 0.5 0.3 0.3 0.0
IQ 0.3 0.5 1.0 −0.2 −0.1 −0.3
FMR1 −0.9 0.3 −0.2 1.0 0.9 1.0
FMR1-205 −0.8 0.3 −0.1 0.9 1.0 0.8
FMR1-217 −1.0 0.0 −0.3 1.0 0.8 1.0
In Table 12, +/− 0-0.1: no correlation; +/− 0.1-0.29: weak correlation; +/− 0.3-0.49: moderate correlation; +/− 0.5-1: strong correlation.
Example 5. FMR1-217 is Expressed in Human FXS and Pre-Mutation Carrier Postmortem Brain To investigate whether FMR1-217 is expressed in FXS brain, publicly available RNA-seq data of post-mortem frontal cortex tissues from FXS individuals (CGG repeats >200), FXS carriers (CGG repeats 55-200) and TD individuals (CGG repeats <55) (Tran et al., 2019) were analyzed. FMR1 RNA (TPM) levels are highest in pre-mutation carriers (FIG. 31). Interestingly, the FXS sample UMB5746 also displays high levels of FMR1 RNA (FIGS. 31 and 32A). This analysis shows that this individual expressed FMR1-217 as did FXS carrier UMB5212, who had Fragile X-associated tremor/ataxia syndrome (FXTAS) (FIGS. 31 and 32A). Neither TD individual had any RNA reads corresponding to FMR1-217 (FIGS. 31 and 32A). Thus, FMR1-217 RNA may be expressed in the brains of a subset of FXS individuals and premutation carriers.
A BLAST analysis showed that FMR1-217 aligned only with intron 1 of FMR1 and with no other region of the genome. Additional data showed unequivocally that FMR1-217 is derived from FMR1, and that its synthesis is dependent the CGG expansion in this gene. Vershkov et al. used CRISPR/Cas9 to delete the CGG expansion from FMR1 in FXS iPSC-derived neural stem cells (NSCs). Additional FXS NSCs were incubated with 5-AzadC, a nucleoside analogue that prevents DNA methylation. RNA sequencing from these samples, as well as from FXS NSCs incubated with vehicle, was then performed. The RNA-seq data from Vershkov et al. was reanalyzed, some of which is presented in FIG. 32B, and FMR1 transcript quantification (TPM) in Table 13. RNA-seq reads corresponding to FMR1-217 were clearly evident in the FXS-NSCs incubated with 5-AzadC, but not in the other samples. Moreover, the CGG edited cells, which were isogenic to the unedited FXS NSCs, had no FMR1-217 reads, but instead robust expression of full-length FMR1. Quantification of the RNA-seq reads (TPM) showed strong total FMR1 and FMR1-205 expression in the CGG-edited and 5-AzadC-treated cells but not in vehicle-treated cells. More importantly, strong FMR1-217 expression was observed only in the 5-AzadC-treated cells. Therefore, FMR1-217 is derived from the FMR1 locus and requires a CGG expansion.
TABLE 13
FMR1 (Total, −205 or −217) reads
(TPM) of the samples in FIG. 32B
FMR1 FMR1-205 FMR1-217
Vehicle 0.0 0.0 0.0
Vehicle 0.2 0.0 0.0
5-AzadC 9.9 0.8 6.9
5-AzadC 6.1 1.9 3.9
CGG edited 27.1 3.1 0.1
CGG edited 33.0 7.6 0.3
In a complementary study, Liu et al. performed a targeted FMR1 gene demethylation experiment by incubating FXS iPSC and FXS iPSC-derived neurons with a FMR1 small guide RNA and a catalytically inactive Cas9 fused to Tet1 demethylase sequences. Reanalysis of the subsequent RNA-seq data is shown in FIG. 32C, and FMR1 transcript quantification (TPM) in Table 8. Their experimental paradigm showed that FMR1-217 sequences were evident only when the gene was demethylated in the FXS cells. Quantification of the relevant transcripts in Table 14 showed that strong FMR1 and FMR1-205 expression was detected in the Tet1-treated samples (but inexplicably, no FMR1-205 in sample N1_Tet1), and FMR1-217 expression in all Tet1-treated samples. These data therefore show once again that FMR1-217 is derived from the FMR1 locus and requires a CGG expansion.
TABLE 14
FMR1 (Total, 205 or 217) reads (TPM)
of the samples in FIG. 32C.
FMR1 FMR1-205 FMR1-217
i_mock 0.1 0.0 0.0
i_Tet1 69.9 0.0 7.3
N1_mock 0.1 0.0 0.0
N2_mock 0.1 0.0 0.0
N1_Tet1 46.4 0.0 6.9
N2_Tet1 81.3 22.7 13.3
N3_Tet1 50.4 12.3 10.6
To determine whether transcriptome-wide changes in RNA expression could be detected in the frontal cortex RNA-seq data (Tran et al., 2019) from the FXS vs. TD or FXS vs. FXS carriers, DGE, DAS, and APA analysis was performed. Although the sample size is small, comparing FXS samples 103108GP and JS03 to TD samples UCD1407 and 103710XX (FIG. 31), changes in the levels of 78 RNAs (FIG. 33; 69 down-regulated and 9 up-regulated), 351 differential alternative splicing events (FIG. 34), and 1072 changes in 3′UTR length (FIG. 40; 255 long 3′UTR-distal poly(A) and 817 short 3′UTR-proximal poly(A)) were found. A comparison of FXS samples UMB5319 and UMB5746 to FXS carrier samples UMB5212 and UMB5529 (FIG. 31) shows that the levels of 26 RNAs (FIG. 41; 16 down-regulated and 10 up-regulated), 204 differential alternative splicing events (FIG. 34), and 244 changes in 3′UTR length (FIG. 42; 112 long 3′UTR-distal poly(A) and 132 3′UTR-proximal poly(A)) were altered in a statistically significant manner. Thus, in the available dataset, hundreds of transcriptomic changes are evident in brain tissue from FXS individuals and FXS carriers.
To confirm expression of FMR1-217 RNA in FXS brain tissue, frozen post-mortem cortex samples from six FXS males and five age-matched typically developing (TD) males (UC Davis Health) were obtained. Using RT-qPCR it was found that the FMR1 full length RNA was significantly reduced in the FXS individuals compared to that in the TD individuals. However, 3 or 4 of the 6 FXS individuals expressed varying levels of the FMR1 full-length RNA and also the FMR1-217 RNA (1031-09LZ, 1001-18DL and 1033-08WS) (FIG. 35). Expression of FMR1 RNA has been described previously for the sample 1031-09LZ (Esanov et al., 2016). The two FXS tissue samples (1031-08GP and JS03) studied in Tran et al, did not show FMR1 RNA expression as seen previously (FIGS. 31 and 35).
FMR1-217 RNA was detected in only one of the two premutation carrier samples. To gain greater insight into the relationship of FMR1-217 FXS carrier tissue (CGG repeats between 55-200), skin biopsies from 3 additional premutation carriers and 3 TD individuals (FIG. 36) were obtained. The skin samples were cultured in vitro to generate fibroblast cell lines for RNA analysis. Interestingly, using RT-qPCR cycle threshold (ct) traces from technical replicates, we detected FMR1-217 in one premutation carrier (C172) with 140 CGG repeats but not in samples with 77 or 98 CGG repeats (FIG. 36). There was no change in total FMR1 RNA levels among the samples (FIG. 36). Thus, generation of FMR1-217 may be linked to the number of CGG repeats in the FMR1 gene.
Example 6. FMR1-217 RNA is Expressed in Lymphoblast Cell Cultures from FXS Individuals DNA methylation of the CpG island upstream of the FMR1 gene promoter in FXS individuals (MFM, Methylated full mutation) contributes to transcriptional silencing of the locus and loss of FMRP. FMR1 transcription can be reactivated by treatment with the nucleoside analogue 5-AzadC (5-aza-2′-deoxycytidine), which inhibits DNA methylation (Tabolacci et al., 2016b, 2016a). Consequently, whether re-activating FMR1 transcription in cells from FXS individuals with a presumably fully methylated and completely silenced FMR1 locus results in FMR1-217 expression was investigated. For these experiments, lymphoblast cell lines (LCLs) derived from a FXS individual with a fully methylated locus (MFM) that is transcriptionally inactive (FXS1, GM07365), a FXS individual with a presumably partially methylated locus (UFM) that expresses some FMR1 RNA (FXS2, GM06897), and two typically developing individuals (TD1, GM07174, and TD2, GM06890) (all samples from Corriell Institute, NJ, USA) (FIG. 37) were used. Western blot analysis shows that modest levels of FMRP are detected in FXS2, but not FXS1 cell lines. FMRP is strongly expressed in TD1 and TD2 cells (ratios of FMRP/GAPDH relative to TD2 are shown below the blot) (FIG. 37). Using RT-qPCR, it was found that FMR1-217 RNA is expressed in FXS2 LCLs and comprises 56% of the total FMR1 RNA compared to only 9% in TD cells (FIG. 38). It is noteworthy that although total FMR1 RNA levels in FXS2 cells are similar to those in TD cells, FMRP levels are much lower (FIGS. 37 and 38). Next, FXS1 and FXS2 cell lines were treated with the 5-AzadC and then measured FMR1 RNA and FMRP levels. In the FXS1 cell line, treatment with 5-AzadC for seven days resulted in significant increases of both full-length FMR1 and FMR1-217 RNAs relative to DMSO-treated cells (FIG. 39). However, in FXS2 cells, 5-AzadC treatment resulted in an increase of only full-length FMR1 RNA (FIG. 33). In neither cell line did 5-AzadC treatment induce an increase in FMRP (bottom panel of FIG. 39). Therefore, demethylation of fully methylated FMR1 induces FMR1-217 RNA expression. Most importantly, transcriptional activation of normally silenced FMR1 by demethylation alone does no commensurately induce FMRP expression.
TABLE 1
Non-Limiting Examples of RNA Markers with Increased Expression in FXS
Gene symbol ENSEMBL Gene ID log2FoldChange pvalue padj
FAM3B ENSG00000183844 5.94 0.000037 0.004264
XKR3 ENSG00000172967 2.80 0.000125 0.008997
MAP3K15 ENSG00000180815 2.08 0.000115 0.008550
LEP ENSG00000174697 2.03 0.000780 0.027134
RP11-706O15.3 nan 1.97 0.001652 0.039687
GCOM1 ENSG00000137878 1.96 0.000285 0.015209
CXCL6 ENSG00000124875 1.47 0.000001 0.000440
RGL3 ENSG00000205517 1.43 0.000008 0.001802
NECAB2 ENSG00000103154 1.41 0.000030 0.003899
TGM3 ENSG00000125780 1.41 0.000176 0.011573
LRRC6 ENSG00000129295 1.31 0.000013 0.002488
MAB21L3 ENSG00000173212 1.31 0.000979 0.030144
RP11-36B15.1 nan 1.29 0.001360 0.036019
AC091878.1 nan 1.27 0.001202 0.033616
RP11-154H23.3 nan 1.27 0.000120 0.008698
NOV ENSG00000136999 1.26 0.000020 0.003000
AC093495.4 nan 1.23 0.000161 0.010925
RP11-455F5.6 nan 1.22 0.000153 0.010637
RGPD2 ENSG00000185304 1.21 0.000081 0.006732
COL9A3 ENSG00000092758 1.21 0.000580 0.023121
CLEC18A ENSG00000157322 1.19 0.002008 0.045512
RP11-256L6.2 nan 1.16 0.000829 0.027666
LINC01127 ENSG00000281162 1.15 0.000037 0.004264
SLC38A11 ENSG00000169507 1.14 0.000595 0.023337
EFCAB12 ENSG00000172771 1.12 0.000427 0.019671
LA16c-380H5.5 nan 1.10 0.000155 0.010758
CXCL1 ENSG00000163739 1.10 0.001537 0.038485
RP11-1334A24.5 nan 1.10 0.000012 0.002357
AC100793.2 nan 1.07 0.000005 0.001405
ANKDD1A ENSG00000166839 1.07 0.000081 0.006732
AVIL ENSG00000135407 1.06 0.000089 0.007105
RP11-44F14.8 nan 1.03 0.000021 0.003068
RP11-290F20.1 nan 1.03 0.000426 0.019671
AC116366.5 nan 1.03 0.000023 0.003198
EPHB4 ENSG00000196411 1.02 0.000000 0.000003
ST6GALNAC3 ENSG00000184005 1.02 0.001602 0.039149
PANX2 ENSG00000073150 1.01 0.000000 0.000081
CREB5 ENSG00000146592 1.01 0.000018 0.002853
KIAA0319 ENSG00000137261 1.00 0.000145 0.010196
HECW2 ENSG00000138411 0.99 0.000041 0.004422
ADCY4 ENSG00000129467 0.99 0.000001 0.000346
LINC00173 ENSG00000196668 0.99 0.000055 0.005277
RP11-59D5_B.2 nan 0.99 0.000001 0.000408
RP11-274B18.2 nan 0.97 0.001709 0.040781
RP11-213H15.3 nan 0.97 0.000002 0.000670
CORO7-PAM16 ENSG00000103426 0.97 0.000004 0.001204
HAL ENSG00000084110 0.95 0.000013 0.002488
DPEP3 ENSG00000141096 0.95 0.000035 0.004173
AC002467.7 nan 0.95 0.000859 0.028282
MGAM ENSG00000257335 0.95 0.000265 0.014805
TABLE 2
Non-Limiting Examples of RNA Markers with Reduced Expression in FXS
Gene symbol ENSEMBL Gene ID log2FoldChange pvalue padj
S100B ENSG00000160307 −3.34 1.23E−07 0.00013926
RP11-885N19.6 nan −3.11 8.50E−05 0.00695513
RP11-545I5.3 nan −2.78 0.00171979 0.04085578
AC091814.2 nan −2.52 0.00067871 0.02508099
KLRC2 ENSG00000205809 −2.45 0.00063287 0.02384782
L1TD1 ENSG00000240563 −2.41 1.70E−07 0.00015287
PGBD5 ENSG00000177614 −2.27 0.00027758 0.01511272
MXRA7 ENSG00000182534 −1.93 3.42E−05 0.0041732
CROCC2 ENSG00000226321 −1.86 0.00076619 0.02700921
SEMA5A ENSG00000112902 −1.84 1.60E−06 0.00063283
PLA2G4C ENSG00000105499 −1.83 3.68E−06 0.00112744
RP11-1008C21.1 nan −1.83 0.00077192 0.02708609
TANC1 ENSG00000115183 −1.81 0.00062905 0.02384782
C4orf50 ENSG00000181215 −1.79 7.02E−05 0.00610208
NUAK1 ENSG00000074590 −1.76 0.00092774 0.02908497
AC104809.4 nan −1.72 7.07E−05 0.00611524
RGS17 ENSG00000091844 −1.71 0.00118851 0.03348616
KCNS1 ENSG00000124134 −1.69 0.00032366 0.01655409
DRAXIN ENSG00000162490 −1.69 0.00086416 0.02831001
B3GAT1 ENSG00000109956 −1.68 0.00068513 0.02516046
ARHGEF28 ENSG00000214944 −1.63 0.00213167 0.04671591
KIF19 ENSG00000196169 −1.62 0.00115227 0.03276699
APOL4 ENSG00000100336 −1.60 0.00133272 0.03567311
GZMH ENSG00000100450 −1.58 0.00232882 0.04897115
GAS1 ENSG00000180447 −1.52 1.80E−06 0.00067285
SCD5 ENSG00000145284 −1.52 4.62E−07 0.00033415
GLB1L2 ENSG00000149328 −1.50 0.00142343 0.03695763
IGHA1 ENSG00000211895 −1.48 8.12E−10 3.11E−06
KNDC1 ENSG00000171798 −1.45 0.0001015 0.00776551
RP11-383H13.1 nan −1.44 0.00087252 0.02840134
FGFR2 ENSG00000066468 −1.44 1.43E−05 0.00258244
TFCP2L1 ENSG00000115112 −1.43 0.00033156 0.01674834
PDGFRB ENSG00000113721 −1.41 0.0001128 0.00841832
LAG3 ENSG00000089692 −1.38 1.35E−06 0.00058675
GPR153 ENSG00000158292 −1.36 2.96E−05 0.00383882
PODN ENSG00000174348 −1.36 6.61E−05 0.00586108
CKB ENSG00000166165 −1.35 3.44E−05 0.0041732
CERCAM ENSG00000167123 −1.31 3.11E−05 0.00396882
ZNF365 ENSG00000138311 −1.30 0.00026806 0.01480521
JUP ENSG00000173801 −1.28 8.13E−06 0.00182843
TRNP1 ENSG00000253368 −1.28 0.00148083 0.03787471
JAKMIP1 ENSG00000152969 −1.28 1.29E−05 0.00248842
CPXM1 ENSG00000088882 −1.27 0.0011645 0.0330532
SLC1A7 ENSG00000162383 −1.25 0.00025407 0.01434331
LGR6 ENSG00000133067 −1.24 0.00046635 0.02056663
FCRL6 ENSG00000181036 −1.23 0.00076397 0.02700921
MORN4 ENSG00000171160 −1.23 9.68E−05 0.00748928
TUBB2A ENSG00000137267 −1.21 0.00111934 0.03223865
PRSS23 ENSG00000150687 −1.18 9.24E−08 0.00012854
BFSP1 ENSG00000125864 −1.16 0.00018139 0.01165981
TABLE 3
Non-Limiting Examples of RNA Markers with Decreased Exon Skipping in FXS
Gene symbol ENSEMBL Gene ID chr strand PValue FDR IncLevelDifference
NCALD ENSG00000104490 8 − 4.96E−08 1.72E−05 0.505
ZNF573 ENSG00000189144 19 − 2.04E−05 0.00196032 0.339
PAK1 ENSG00000149269 11 − 0.00044025 0.02048598 0.31
MIR4435-2HG ENSG00000172965 2 − 8.29E−05 0.00579463 0.285
CD8B ENSG00000172116 2 − 1.81E−05 0.00177935 0.277
PDGFC ENSG00000145431 4 − 0.000346763 0.01709337 0.264
TRAPPC2L ENSG00000167515 16 + 0.000221258 0.01224535 0.257
AC006504.5 nan 19 + 0.001123229 0.04142531 0.245
ZNF512 ENSG00000243943 2 + 0.000146908 0.00893035 0.232
FAM228B ENSG00000219626 2 + 0.001178813 0.04295611 0.226
NEIL2 ENSG00000154328 8 + 5.13E−05 0.00403721 0.215
FAM78A ENSG00000126882 9 − 0.000593929 0.02558632 0.21
FYB1 ENSG00000082074 5 − 3.81E−06 0.00053168 0.2
RNF216P1 ENSG00000196204 7 + 0.001005397 0.03818502 0.197
ZCWPW1 ENSG00000078487 7 − 0.000637671 0.02697481 0.194
DTX2 ENSG00000091073 7 + 0.000222932 0.01231721 0.187
ATP5MD ENSG00000173915 10 − 0.000189351 0.01083592 0.187
MX2 ENSG00000183486 21 + 0.000241142 0.01307969 0.18
LYRM1 ENSG00000102897 16 + 0.00024572 0.01325809 0.175
GUF1 ENSG00000151806 4 + 0.000727864 0.02995953 0.174
DPH7 ENSG00000148399 9 − 0.000264816 0.01399492 0.173
NSFL1C ENSG00000088833 20 − 3.62E−06 0.00051009 0.169
MTMR1 ENSG00000063601 X + 0.00123067 0.0444019 0.169
GTPBP10 ENSG00000105793 7 + 0.001021594 0.03855642 0.165
RGS3 ENSG00000138835 9 + 8.35E−10 6.81E−07 0.165
Gene symbol exonStart_0base exonEnd upstreamES upstreamEE downstreamES downstreamEE
NCALD 101779923 101779979 101719385 101719648 101887140 101887227
ZNF573 37759046 37759139 37738286 37740194 37770004 37770097
PAK1 77397026 77397093 77392442 77392541 77408153 77408232
MIR4435-2HG 111247429 111247558 111239801 111239996 111248147 111248241
CD8B 86822320 86822374 86815346 86815718 86844921 86844958
PDGFC 156861428 156861489 156850220 156850416 156970785 156971315
TRAPPC2L 88859344 88859443 88858618 88858789 88859892 88859972
AC006504.5 27797753 27798176 27793430 27793650 27805604 27805811
ZNF512 27583657 27583716 27582968 27583142 27598069 27598254
FAM228B 24167626 24167683 24164197 24164335 24169355 24169496
NEIL2 11770173 11770335 11769698 11769791 11771445 11771585
FAM78A 131263477 131263599 131258075 131261350 131270459 131270523
FYB1 39212677 39213017 39202773 39202987 39274402 39274528
RNF216P1 4995474 4995582 4984909 4985075 4996609 4996673
ZCWPW1 100401888 100402041 100400852 100401336 100403693 100403785
DTX2 76497336 76497477 76492152 76492253 76500440 76500520
ATP5MD 103394198 103394394 103392370 103392466 103395745 103396032
MX2 41373897 41374127 41370212 41370645 41376835 41376949
LYRM1 20902485 20902717 20900449 20900535 20920121 20920214
GUF1 44688006 44688146 44686509 44686713 44689285 44689409
DPH7 137577576 137577603 137576308 137576402 137578624 137578717
NSFL1C 1472714 1473012 1464328 1464426 1473791 1473842
MTMR1 150751029 150751240 150750729 150750843 150762564 150762737
GTPBP10 90354457 90354549 90352815 90353009 90372154 90372228
RGS3 113565514 113565730 113536795 113536918 113583449 113584427
TABLE 4
Non-Limiting Examples of RNA Markers with Increased Exon Skipping in FXS
Gene symbol ENSEMBL Gene ID chr strand PValue FDR IncLevelDifference
NCALD ENSG00000104490 8 − 5.33E−15 2.91E−11 −0.504
DRAM2 ENSG00000156171 1 − 2.71E−13 9.60E−10 −0.441
NCALD ENSG00000104490 8 − 2.24E−07 5.54E−05 −0.435
RHOH ENSG00000168421 4 + 0.000779534 0.031522709 −0.374
LAIR2 ENSG00000167618 19 + 5.36E−06 0.000699899 −0.363
GBP3 ENSG00000117226 1 − 7.09E−09 3.66E−06 −0.359
GTF2H1 ENSG00000110768 11 + 0.000513829 0.022997385 −0.353
XPNPEP3 ENSG00000196236 22 + 2.97E−09 1.81E−06 −0.336
DRAM2 ENSG00000156171 1 − 3.11E−09 1.86E−06 −0.308
ZNF888 ENSG00000213793 19 − 0.000197457 0.011192452 −0.295
TBC1D5 ENSG00000131374 3 − 0.000208142 0.011652147 −0.279
AC060780.1 nan 17 − 0.000132965 0.008300559 −0.276
SDHAP2 ENSG00000215837 3 + 8.95E−11 1.18E−07 −0.254
KMT2A ENSG00000118058 11 + 2.66E−06 0.000398951 −0.237
SH3BP2 ENSG00000087266 4 + 3.42E−09 2.00E−06 −0.226
TBC1D5 ENSG00000131374 3 − 0.000917527 0.035663172 −0.225
CSNK1G2 ENSG00000133275 19 + 4.33E−05 0.003529449 −0.214
ATP5MD ENSG00000173915 10 − 0.000573727 0.025011619 −0.214
NSUN5P1 ENSG00000223705 7 + 2.96E−06 0.000432046 −0.204
LINC01128 ENSG00000228794 1 + 0.00014825 0.008981293 −0.204
RNF19A ENSG00000034677 8 − 1.09E−05 0.001206693 −0.194
SNHG8 ENSG00000269893 4 + 0.000256909 0.013715154 −0.189
SNHG8 ENSG00000269893 4 + 0.000178693 0.010366148 −0.182
TOP1MT ENSG00000184428 8 − 0.001185002 0.043130386 −0.178
AL135818.1 nan 14 + 0.000537267 0.023809757 −0.174
Gene symbol exonStart_0base exonEnd upstreamES upstreamEE downstreamES downstreamEE
NCALD 101887140 101887227 101719251 101719648 101915808 101915858
DRAM2 111139587 111139711 111137522 111137586 111140037 111140062
NCALD 101887140 101887227 101779923 101779979 101915808 101915858
RHOH 40235192 40235358 40193662 40193812 40242713 40242834
LAIR2 54509034 54509085 54507890 54508184 54510525 54510687
GBP3 89010903 89011116 89009391 89009494 89013184 89013427
GTF2H1 18325946 18326153 18324235 18324296 18333059 18333183
XPNPEP3 40860677 40860793 40857096 40857245 40861617 40862770
DRAM2 111139500 111139666 111137522 111137586 111140037 111140090
ZNF888 52918818 52918937 52917858 52917931 52923368 52923481
TBC1D5 17622647 17622765 17562018 17562142 17623848 17623913
AC060780.1 43166979 43167849 43148367 43148783 43170125 43170316
SDHAP2 195663623 195663767 195662570 195662733 195664085 195664250
KMT2A 118439023 118439122 118436509 118436944 118468774 118468844
SH3BP2 2794162 2794262 2793084 2793138 2796373 2796646
TBC1D5 17518901 17518995 17508473 17508605 17562018 17562142
CSNK1G2 1968790 1968905 1942458 1942613 1969507 1969959
ATP5MD 103395745 103396032 103394198 103394394 103396408 103396475
NSUN5P1 75414639 75414798 75412788 75412932 75414884 75415024
LINC01128 841199 841373 829002 829104 851926 852110
RNF19A 100300527 100300651 100287500 100288267 100303159 100303259
SNHG8 118278943 118279137 118278754 118278792 118279388 118279431
SNHG8 118278933 118279137 118278754 118278792 118279388 118279431
TOP1MT 143332486 143332657 143331223 143331339 143334107 143334285
AL135818.1 91247489 91247659 91244354 91244499 91250764 91251228
TABLE 5
Non-Limiting Examples of RNA Markers with Decreased Mutually Exclusive Exon (MXE) Switching in FXS
Gene symbol ENSEMBL Gene ID chr strand PValue FDR IncLevelDifference
CR1 ENSG00000203710 chr1 + 5.69E−06 0.000783263 0.395
CRIM1 ENSG00000150938 chr2 + 8.09E−07 0.00015988 0.271
ZCWPW1 ENSG00000078487 chr7 − 4.05E−07 8.88E−05 0.262
NAP1L1 ENSG00000187109 chr12 − 0.000173204 0.01078021 0.238
TBC1D5 ENSG00000131374 chr3 − 0.001307502 0.046275622 0.237
MIR4435-2HG ENSG00000172965 chr2 − 0.00102711 0.038876331 0.236
AC004593.2 nan chr7 + 5.31E−05 0.004472215 0.235
GBP3 ENSG00000117226 chr1 − 0.000729866 0.030625267 0.222
SEC61A2 ENSG00000065665 chr10 + 0.000855726 0.034366856 0.22
PCNX2 ENSG00000135749 chr1 − 6.98E−05 0.0054603 0.215
NAP1L1 ENSG00000187109 chr12 − 0.000695123 0.029500582 0.206
TPT1-AS1 ENSG00000170919 chr13 + 8.19E−05 0.006166312 0.195
HLA-A ENSG00000206503 chr6 + 9.84E−05 0.007006027 0.179
HLA-A ENSG00000206503 chr6 + 9.64E−05 0.006902919 0.178
LUCAT1 ENSG00000248323 chr5 − 0.000404613 0.020312094 0.176
PTPN2 ENSG00000175354 chr18 − 0.000173086 0.01078021 0.174
SEC31B ENSG00000075826 chr10 − 2.17E−05 0.002275108 0.168
POLR2J3 ENSG00000168255 chr7 − 0.000306057 0.01649295 0.164
POLR2J4 ENSG00000214783 chr7 − 5.42E−05 0.00453613 0.157
CAST ENSG00000153113 chr5 + 5.09E−08 1.72E−05 0.148
POLR2J4 ENSG00000272655 chr7 − 0.000252606 0.014256911 0.147
NUMBL ENSG00000105245 chr19 − 0.000888058 0.035038326 0.144
PRMT7 ENSG00000132600 chr16 + 0.000272932 0.015030406 0.143
ATF7IP2 ENSG00000166669 chr16 + 0.001005564 0.038178258 0.14
TIMM23B-AGAP6 ENSG00000178440 chr10 + 2.60E−08 9.71E−06 0.138
Gene name 1stExonStart_0base 1stExonEnd 2ndExonStart_0base 2ndExonEnd upstreamES upstreamEE downstreamES downstreamEE
CR1 207526752 207526929 207545307 207545484 207523610 207524009 207545575 207545678
CRIM1 36522091 36522313 36537351 36537546 36517326 36517542 36544375 36544498
ZCWPW1 100403693 100403785 100404177 100404244 100400872 100401336 100405012 100405093
NAP1L1 76060137 76060279 76074202 76074239 76056032 76056161 76084566 76084685
TBC1D5 17518901 17518995 17562018 17562142 17508473 17508605 17586352 17586557
MIR4435- 111239801 111239996 111247429 111247558 111233627 111233739 111248147 111248241
2HG
AC004593.2 29146848 29146960 29354624 29354663 29145853 29146745 29367931 29367987
GBP3 89011746 89012027 89013184 89013427 89010903 89011116 89014082 89014279
SEC61A2 12149594 12149726 12149851 12149961 12143116 12143195 12156906 12157067
PCNX2 233139713 233139855 233160282 233160433 233134783 233135190 233161270 233161363
NAP1L1 76067370 76067473 76074202 76074239 76050530 76050653 76084566 76084735
TPT1-AS1 45383090 45383235 45389734 45389820 45378529 45380001 45390713 45390902
HLA-A 29942756 29943543 29944121 29944397 29942551 29942626 29944499 29944616
HLA-A 29942756 29943026 29944121 29944397 29942244 29942626 29944499 29944634
LUCAT1 91303872 91303971 91312294 91312495 91302730 91303161 91313077 91313229
PTPN2 12819213 12819282 12821335 12821425 12814202 12814355 12825809 12825944
SEC31B 100490007 100490322 100495384 100495546 100489702 100489761 100496257 100496431
POLR2J3 102544705 102544776 102566581 102566736 102541500 102541662 102566996 102567083
POLR2J4 43986600 43986677 43987677 43987888 43973209 43973323 43988085 43988247
CAST 96740037 96740118 96740744 96740783 96737848 96737947 96741265 96741358
POLR2J4 43986600 43986677 44013592 44013679 43973209 43973323 44014605 44014783
NUMBL 40673343 40673649 40677231 40677421 40669897 40670020 40680916 40681057
PRMT7 68312041 68312176 68315896 68316074 68310973 68311099 68329065 68329174
ATF7IP2 10473922 10473989 10480878 10480964 10473478 10473534 10481835 10483637
TIMM23B- 49987164 49987234 49988750 49988938 49973011 49973142 49989307 49989376
AGAP6
TABLE 6
Non-Limiting Examples of RNA Markers with Increased Mutually Exclusive Exon (MXE) Switching in FXS
Gene
symbol ENSEMBL Gene ID chr strand PValue FDR IncLevelDifference
HLA-A ENSG00000206503 chr6 + 0 0 −0.569
HLA-A ENSG00000206503 chr6 + 0 0 −0.503
HLA-A ENSG00000206503 chr6 + 0 0 −0.482
HLA-A ENSG00000206503 chr6 + 0 0 −0.478
HLA-A ENSG00000206503 chr6 + 0 0 −0.469
HLA-A ENSG00000206503 chr6 + 0 0 −0.332
ADGRE2 ENSG00000127507 chr19 − 0.000111359 0.007655312 −0.298
PAK1 ENSG00000149269 chr11 − 0.000566363 0.025601762 −0.294
TBC1D5 ENSG00000131374 chr3 − 6.39E−05 0.005090138 −0.272
GTF2H2B ENSG00000226259 chr5 + 0.001061621 0.039866163 −0.26
MICA ENSG00000204520 chr6 + 2.23E−06 0.000369146 −0.24
SLC29A2 ENSG00000174669 chr11 − 0.001359543 0.047413746 −0.225
HLA-A ENSG00000206503 chr6 + 1.60E−07 4.19E−05 −0.209
ZBTB10 ENSG00000205189 chr8 + 0.000213606 0.012757245 −0.195
NLGN3 ENSG00000196338 chrX + 0.001294693 0.045950152 −0.194
CAST ENSG00000153113 chr5 + 1.16E−08 4.98E−06 −0.187
METTL25 ENSG00000127720 chr12 + 1.66E−05 0.001861552 −0.186
MICA ENSG00000204520 chr6 + 0.000904573 0.0353971 −0.181
ADAM15 ENSG00000143537 chr1 + 0.000177579 0.011034472 −0.179
LUCAT1 ENSG00000248323 chr5 − 0.000129664 0.008649685 −0.17
TBC1D5 ENSG00000131374 chr3 − 6.26E−05 0.005018258 −0.167
SSH1 ENSG00000084112 chr12 − 5.43E−06 0.00075397 −0.159
ADAM15 ENSG00000143537 chr1 + 0.00025982 0.014540534 −0.156
SIRPB1 ENSG00000101307 chr20 − 6.72E−07 0.000137064 −0.156
GBP3 ENSG00000117226 chr1 − 9.61E−09 4.26E−06 −0.155
Gene
name 1stExonStart_0base 1stExonEnd 2ndExonStart_0base 2ndExonEnd upstreamES upstreamEE downstreamES downstreamEE
HLA-A 29944121 29944397 29944499 29945091 29943284 29943543 29945233 29945281
HLA-A 29944121 29944397 29945058 29945091 29942756 29943543 29945233 29945281
HLA-A 29944499 29944616 29945233 29945281 29944121 29944397 29945450 29945870
HLA-A 29944121 29944397 29944499 29944616 29942756 29943543 29945058 29945091
HLA-A 29944499 29945091 29945233 29945281 29944121 29944397 29945450 29945884
HLA-A 29945058 29945091 29945233 29945281 29944499 29944616 29945450 29945870
ADGRE2 14754953 14755127 14755653 14755844 14751435 14751671 14756237 14756345
PAK1 77397026 77397158 77408153 77408232 77392330 77392541 77411773 77411933
TBC1D5 17562018 17562142 17622647 17622765 17508473 17508605 17623848 17623913
GTF2H2B 70434914 70435022 70437530 70437594 70434178 70434266 70440755 70440859
MICA 31411071 31411359 31412324 31412460 31410542 31410797 31415011 31415313
SLC29A2 66366125 66366231 66366430 66366564 66365935 66366021 66367463 66367548
HLA-A 29943267 29943543 29944499 29944616 29942756 29943026 29945058 29945091
ZBTB10 80499493 80500382 80513909 80514008 80486212 80487782 80518402 80518438
NLGN3 71164142 71164328 71167010 71167800 71155213 71155363 71169253 71171199
CAST 96740744 96740783 96741265 96741358 96740037 96740118 96741493 96741580
METTL25 82456726 82456820 82476643 82476718 82438514 82438791 82477280 82477352
MICA 31411071 31411359 31411946 31412225 31410542 31410797 31412324 31412460
ADAM15 155061417 155061489 155061903 155062117 155060204 155060343 155062244 155062369
LUCAT1 91244819 91245010 91264662 91264713 91242940 91243002 91313637 91313777
TBC1D5 17428449 17428519 17622647 17622765 17406417 17406526 17623848 17623913
SSH1 108817037 108817159 108818248 108818313 108811259 108811328 108823257 108823361
ADAM15 155061414 155061489 155061903 155062117 155060204 155060343 155062244 155062369
SIRPB1 1566152 1566267 1578337 1578694 1564383 1565497 1588559 1588632
GBP3 89009391 89009494 89011746 89012027 89008946 89009140 89013184 89013427
TABLE 7
Non-Limiting Examples of RNA Markers with Decreased Alternative 5′ Splice Site (A5SS) in FXS
Gene symbol ENSEMBL Gene ID chr strand PValue FDR IncLevelDifference
PARP2 ENSG00000129484 chr14 + 1.47E−07 3.50E−05 0.307
PACRGL ENSG00000163138 chr4 + 0.001882993 0.04083963 0.252
ENTPD1-AS1 ENSG00000226688 chr10 − 0.000135031 0.005969913 0.217
NEIL2 ENSG00000154328 chr8 + 0.000411623 0.01332848 0.203
FUZ ENSG00000010361 chr19 − 0.000734977 0.020946846 0.184
SDR39U1 ENSG00000100445 chr14 − 0.00031298 0.010957462 0.147
ADAM15 ENSG00000143537 chr1 + 0.000445416 0.014027548 0.14
SDR39U1 ENSG00000100445 chr14 − 0.000206025 0.00799062 0.136
EPOR ENSG00000187266 chr19 − 0.002400735 0.048843263 0.118
ZSCAN26 ENSG00000197062 chr6 + 0.001112686 0.027805061 0.113
SNHG17 ENSG00000196756 chr20 − 0.001199516 0.029028276 0.113
GPS2 ENSG00000132522 chr17 − 0.001308916 0.031129638 0.106
NECAP1 ENSG00000089818 chr12 + 0.001379215 0.032576878 0.094
MRPL11 ENSG00000174547 chr11 − 0.00088251 0.023776073 0.086
DNAJC19 ENSG00000205981 chr3 − 0.000221009 0.008421537 0.085
ANKZF1 ENSG00000163516 chr2 + 0.00119272 0.029005238 0.084
C1orf162 ENSG00000143110 chr1 + 4.88E−06 0.000521701 0.077
PIGT ENSG00000124155 chr20 + 0.000340165 0.011790904 0.073
SLC25A37 ENSG00000147454 chr8 + 0.000418079 0.01347424 0.069
AP1G1 ENSG00000166747 chr16 − 2.01E−05 0.001448127 0.061
CIC ENSG00000079432 chr19 + 0.001042232 0.026722204 0.06
ITGB7 ENSG00000139626 chr12 − 1.90E−05 0.001398195 0.059
ATG16L2 ENSG00000168010 chr11 + 1.46E−06 0.000214648 0.058
BECN1 ENSG00000126581 chr17 − 0.000617385 0.018137461 0.056
ARHGEF40 ENSG00000165801 chr14 + 0.002236606 0.046323946 0.053
Gene symbol longExonStart_0base longExonEnd shortES shortEE flankingES flankingEE
PARP2 20344931 20345126 20344931 20345087 20345393 20345464
PACRGL 20700457 20700787 20700457 20700611 20704465 20704533
ENTPD1-AS1 95907662 95907903 95907777 95907903 95904829 95904938
NEIL2 11769709 11770335 11769709 11769791 11771445 11771585
FUZ 49812446 49812736 49812637 49812736 49812250 49812335
SDR39U1 24442108 24442260 24442177 24442260 24440782 24440926
ADAM15 155061903 155062117 155061903 155061975 155062244 155062369
SDR39U1 24442097 24442260 24442177 24442260 24440782 24440926
EPOR 11382846 11383232 11383096 11383232 11381929 11382105
ZSCAN26 28271853 28272336 28271853 28271934 28272669 28272787
SNHG17 38435026 38435352 38435196 38435352 38434503 38434626
GPS2 7313567 7313988 7313905 7313988 7313211 7313291
NECAP1 8090194 8091850 8090194 8090299 8092675 8092784
MRPL11 66438631 66438848 66438709 66438848 66438163 66438259
DNAJC19 180986947 180987022 180986997 180987022 180985925 180985996
ANKZF1 219230227 219230405 219230227 219230350 219232259 219232362
C1orf162 111476797 111477078 111476797 111476867 111477650 111477775
PIGT 45416516 45416694 45416516 45416654 45419294 45419395
SLC25A37 23566107 23566813 23566107 23566336 23568321 23568378
AP1G1 71808504 71808832 71808762 71808832 71789278 71789482
CIC 42294172 42294304 42294172 42294298 42294603 42294735
ITGB7 53201117 53201194 53201146 53201194 53200242 53200446
ATG16L2 72822477 72823797 72822477 72822543 72824059 72824122
BECN1 42824132 42824282 42824154 42824282 42823747 42823879
ARHGEF40 21075331 21075765 21075331 21075499 21076359 21076456
TABLE 8
Non-Limiting Examples of RNA Markers with Increased Alternative 5′ Splice Site (A5SS) in FXS
Gene symbol ENSEMBL Gene ID chr strand PValue FDR IncLevelDifference
BANP ENSG00000172530 chr16 + 3.92E−05 0.002371624 −0.251
PIGA ENSG00000165195 chrX − 0.001051527 0.026841331 −0.23
SNHG8 ENSG00000269893 chr4 + 0.00023797 0.008824083 −0.183
PIGA ENSG00000165195 chrX − 0.001803685 0.039617882 −0.172
RAD52 ENSG00000002016 chr12 − 1.03E−05 0.000910652 −0.152
IRF3 ENSG00000126456 chr19 − 0.001145703 0.028226011 −0.131
CEP78 ENSG00000148019 chr9 + 1.28E−07 3.27E−05 −0.115
SPINT1 ENSG00000166145 chr15 + 0.001017573 0.026722204 −0.103
TMEM156 ENSG00000121895 chr4 − 8.68E−06 0.000801041 −0.095
NT5C3B ENSG00000141698 chr17 − 1.67E−09 1.28E−06 −0.081
PLD2 ENSG00000129219 chr17 + 0.001405759 0.032977951 −0.079
HLA-A ENSG00000206503 chr6 + 1.24E−06 0.000194652 −0.078
ANKRD12 ENSG00000101745 chr18 + 6.58E−08 1.89E−05 −0.074
CASP8 ENSG00000064012 chr2 + 0.000112282 0.005162722 −0.071
PACS2 ENSG00000179364 chr14 + 0.000167594 0.007048141 −0.069
HLA-DMA ENSG00000204257 chr6 − 0.00151269 0.034776744 −0.066
DHPS ENSG00000095059 chr19 − 7.10E−05 0.003816051 −0.061
PDCD6 ENSG00000249915 chr5 + 0.002223693 0.046323946 −0.057
Gene symbol longExonStart_0base longExonEnd shortES shortEE flankingES flankingEE
BANP 87975047 87975207 87975047 87975203 87981035 87981127
PIGA 15331589 15331992 15331873 15331992 15325913 15326046
SNHG8 118278708 118279137 118278708 118278792 118279388 118279431
PIGA 15331215 15331992 15331873 15331992 15325913 15326046
RAD52 914410 914532 914430 914532 913893 914121
IRF3 49664442 49664673 49664552 49664673 49663342 49663514
CEP78 78236079 78236659 78236079 78236603 78240022 78240195
SPINT1 40853710 40853929 40853710 40853881 40854059 40854086
TMEM156 38998622 38998909 38998639 38998909 38993737 38993998
NT5C3B 41835587 41835957 41835858 41835957 41835202 41835272
PLD2 4819428 4819582 4819428 4819549 4821792 4821907
HLA-A 29944499 29944634 29944499 29944616 29945058 29945091
ANKRD12 9208656 9208803 9208656 9208797 9211583 9211784
CASP8 201276826 201277104 201276826 201276968 201284815 201285317
PACS2 105381913 105382058 105381913 105382046 105382476 105382581
HLA-DMA 32949270 32949399 32949273 32949399 32948612 32948868
DHPS 12680149 12680325 12680195 12680325 12679800 12679922
PDCD6 304176 306754 304176 304221 311292 311402
TABLE 9
Non-Limiting Examples of RNA Markers with Decreased Alternative 3′ Splice Site (A3SS) in FXS
Gene symbol ENSEMBL Gene ID chr strand PValue FDR IncLevelDifference
SNX5 ENSG00000089006 chr20 − 0.000194034 0.008919334 0.36
POLR2J3 ENSG00000168255 chr7 − 0.000357592 0.013857389 0.274
MPPE1 ENSG00000154889 chr18 − 0.00065011 0.021232751 0.225
AC016394.2 nan chr10 + 0.000373496 0.014201229 0.224
DPM1 ENSG00000000419 chr20 − 0.002112825 0.049154541 0.215
E2F5 ENSG00000133740 chr8 + 0.000690702 0.022132884 0.193
PTPN7 ENSG00000143851 chr1 − 0.000234758 0.010311143 0.192
MTFP1 ENSG00000242114 chr22 + 0.001427494 0.036640206 0.189
TOR1AIP1 ENSG00000143337 chr1 + 0.001713159 0.041763377 0.18
POT1 ENSG00000128513 chr7 − 0.001333453 0.034930288 0.164
JOSD2 ENSG00000161677 chr19 − 0.000481576 0.017268979 0.162
NLRX1 ENSG00000160703 chr11 + 0.000579012 0.019601762 0.152
FDXR ENSG00000161513 chr17 − 0.001067903 0.02935361 0.14
DPM1 ENSG00000000419 chr20 − 6.02E−06 0.000681358 0.131
ZDHHC16 ENSG00000171307 chr10 + 0.001216023 0.032437883 0.112
ALKBH4 ENSG00000160993 chr7 − 0.000183349 0.00860979 0.109
RPS9 ENSG00000170889 chr19 + 0.000143135 0.007114834 0.097
POLR2J3 ENSG00000168255 chr7 − 0.00027444 0.011701012 0.097
ZNF302 ENSG00000089335 chr19 + 6.14E−05 0.00398418 0.097
TENT4B ENSG00000121274 chr16 + 0.001285955 0.033860147 0.093
ADGRE2 ENSG00000127507 chr19 − 4.35E−08 1.58E−05 0.09
TKT ENSG00000163931 chr3 − 3.23E−05 0.002352711 0.087
CARD8 ENSG00000105483 chr19 − 3.04E−11 3.09E−08 0.085
RBM26 ENSG00000139746 chr13 − 0.000290148 0.012018713 0.078
WSB1 ENSG00000109046 chr17 + 0.000152823 0.007486868 0.077
Gene symbol longExonStart_0base longExonEnd shortES shortEE flankingES flankingEE
SNX5 17953995 17954231 17953995 17954223 17955364 17955475
POLR2J3 102543524 102543702 102543524 102543661 102544705 102544776
MPPE1 11885675 11885912 11885675 11885816 11886916 11887025
AC016394.2 73253800 73254349 73253892 73254349 73252790 73253095
DPM1 50940864 50940955 50940864 50940933 50941104 50941209
E2F5 85212156 85212204 85212159 85212204 85209141 85209409
PTPN7 202158117 202158320 202158117 202158248 202159280 202159454
MTFP1 30427121 30427403 30427239 30427403 30426716 30426844
TOR1AIP1 179889309 179889369 179889312 179889369 179884691 179884769
POT1 124928814 124928999 124928814 124928996 124929793 124929825
JOSD2 50510285 50510448 50510285 50510445 50511074 50511159
NLRX1 119183117 119184016 119183820 119184016 119182093 119182345
FDXR 74866783 74866879 74866783 74866876 74872035 74872107
DPM1 50940864 50940955 50940864 50940933 50941128 50941209
ZDHHC16 97455638 97455783 97455713 97455783 97454713 97454799
ALKBH4 102459603 102459801 102459603 102459710 102464713 102464863
RPS9 54206552 54207647 54207397 54207647 54201486 54201609
POLR2J3 102566996 102568184 102566996 102567083 102569834 102569924
ZNF302 34683151 34683238 34683154 34683238 34682776 34682897
TENT4B 50225097 50225285 50225238 50225285 50224890 50224994
ADGRE2 14755653 14755877 14755653 14755844 14756237 14756345
TKT 53237796 53237921 53237796 53237820 53240250 53240348
CARD8 48232452 48232789 48232452 48232493 48234402 48234543
RBM26 79365577 79365733 79365577 79365718 79366054 79366195
WSB1 27307743 27309272 27309099 27309272 27306781 27306882
TABLE 10
Non-Limiting Examples of RNA Markers with Increased Alternative 3′ Splice Site (A5SS) in FXS
Gene symbol ENSEMBL Gene ID chr strand PValue FDR IncLevelDifference
DDX60L ENSG00000181381 chr4 − 4.07E−10 2.96E−07 −0.305
ATP11A ENSG00000068650 chr13 + 1.90E−06 0.000288722 −0.234
SRGAP2 ENSG00000266028 chr1 + 1.09E−06 0.000194134 −0.201
CEACAM21 ENSG00000007129 chr19 + 8.31E−06 0.000855104 −0.122
COX18 ENSG00000163626 chr4 − 0.00049716 0.017529627 −0.106
WDR47 ENSG00000085433 chr1 − 0.000157279 0.007668305 −0.105
PATZ1 ENSG00000100105 chr22 − 0.000630999 0.020753112 −0.103
POLM ENSG00000122678 chr7 − 0.000406598 0.015121295 −0.097
CC2D1B ENSG00000154222 chr1 − 0.000429204 0.015675962 −0.07
CLK4 ENSG00000113240 chr5 − 0.000414994 0.015321707 −0.069
MIB2 ENSG00000197530 chr1 + 0.000892878 0.026187361 −0.059
PHF1 ENSG00000112511 chr6 + 5.69E−06 0.000666824 −0.058
KANSL1 ENSG00000120071 chr17 − 2.89E−05 0.002165813 −0.051
TCF3 ENSG00000071564 chr19 − 7.88E−07 0.000157428 −0.051
Gene symbol longExonStart_0base longExonEnd shortES shortEE flankingES flankingEE
DDX60L 168395958 168396127 168395958 168396124 168400825 168400978
ATP11A 112881815 112887168 112881875 112887168 112878216 112878303
SRGAP2 206401420 206401645 206401423 206401645 206393544 206393673
CEACAM21 41579269 41579628 41579352 41579628 41577199 41577559
COX18 73064777 73064902 73064777 73064899 73065249 73065413
WDR47 109004591 109004718 109004591 109004715 109010915 109011718
PATZ1 31328786 31328924 31328786 31328859 31335691 31335863
POLM 44074130 44074233 44074130 44074220 44074397 44074530
CC2D1B 52359704 52359883 52359704 52359836 52360073 52360233
CLK4 178619837 178620673 178619837 178619896 178623255 178623416
MIB2 1629033 1629311 1629132 1629311 1628488 1628722
PHF1 33415234 33415329 33415260 33415329 33414724 33414829
KANSL1 46034160 46034285 46034160 46034282 46038537 46038686
TCF3 1619315 1619474 1619315 1619471 1619779 1619853
DDX60L 168395958 168396127 168395958 168396124 168400825 168400978
ATP11A 112881815 112887168 112881875 112887168 112878216 112878303
SRGAP2 206401420 206401645 206401423 206401645 206393544 206393673
CEACAM21 41579269 41579628 41579352 41579628 41577199 41577559
TABLE 15
FMR1 transcript identification and corresponding predicted
amino acid number of encoded protein from ENSEMBL.
Transcript ID Name bp Protein Biotype
ENST00000370475.9 FMR1-205 4441 632aa Protein coding
ENST00000690137.1 FMR1-226 4166 615aa Protein coding
ENST00000218200.12 FMR1-201 4333 611aa Protein coding
ENST00000691111.1 FMR1-228 4154 599aa Protein coding
ENST00000687593.1 FMR1-223 4159 594aa Protein coding
ENST00000439526.6 FMR1-207 3699 592aa Protein coding
ENST00000370470.5 FMR1-203 1774 590aa Protein coding
ENST00000690216.1 FMR1-227 4008 587aa Protein coding
ENST00000440235.6 FMR1-208 4271 586aa Protein coding
ENST00000370477.5 FMR1-206 3437 582aa Protein coding
ENST00000686086.1 FMR1-222 3995 570aa Protein coding
ENST00000691214.1 FMR1-229 4067 569aa Protein coding
ENST00000495717.6 FMR1-212 2874 561aa Protein coding
ENST00000685491.1 FMR1-221 4109 559aa Protein coding
ENST00000621453.5 FMR1-218 1827 548aa Protein coding
ENST00000370471.7 FMR1-204 4125 537aa Protein coding
ENST00000616382.5 FMR1-214 2799 536aa Protein coding
ENST00000692108.1 FMR1-232 4252 509aa Protein coding
ENST00000689517.1 FMR1-224 4484 460aa Protein coding
ENST00000693512.1 FMR1-235 3402 398aa Protein coding
ENST00000334557.10 FMR1-202 1295 297aa Protein coding
ENST00000621987.5 FMR1-219 2440 297aa NMD
ENST00000616614.4 FMR1-215 1409 76aa NMD
ENST00000693452.1 FMR1-234 4093 49aa NMD
ENST00000692091.1 FMR1-231 3908 49aa NMD
ENST00000475038.3 FMR1-209 2747 49aa NMD
ENST00000621447.1 FMR1-217 1832 31aa Protein coding
ENST00000691793.1 FMR1-230 5731 RI
ENST00000492846.2 FMR1-211 5650 RI
ENST00000689570.1 FMR1-225 5650 RI
ENST00000620828.4 FMR1-216 4830 RI
ENST00000693079.1 FMR1-233 4647 RI
ENST00000643620.1 FMR1-220 1439 RI
ENST00000611273.1 FMR1-213 564 RI
ENST00000478848.1 FMR1-210 541 RI
TABLE 16
DE_FXSvsTD
baseMean log2FoldChange lfcSE stat pvalue padj
ANAPC1P2 41.8 24.58 3.17 7.75 9.19E−15 1.70E−10
FAM3B 58.2 5.71 1.04 5.47 4.46E−08 2.91E−04
HMGB1P5 82.4 −1.99 0.36 −5.46 4.73E−08 2.91E−04
CYP4F22 127.3 −1.16 0.23 −5.11 3.15E−07 1.46E−03
RHOC 2690.6 −0.68 0.13 −5.04 4.69E−07 1.56E−03
AGAP1 342.6 −0.99 0.20 −5.02 5.07E−07 1.56E−03
CFAP70 140.9 0.65 0.14 4.61 3.97E−06 1.04E−02
KNDC1 135.2 −1.33 0.29 −4.57 4.82E−06 1.04E−02
PRR5L 1483.6 −0.59 0.13 −4.56 5.05E−06 1.04E−02
ZNF365 105.0 −1.01 0.22 −4.48 7.31E−06 1.35E−02
DUSP5 776.8 −0.62 0.14 −4.29 1.80E−05 2.76E−02
ARHGAP24 601.7 0.54 0.13 4.28 1.84E−05 2.76E−02
EPOP 37.3 −0.92 0.22 −4.27 1.94E−05 2.76E−02
MXRA7 949.6 −1.38 0.32 −4.24 2.24E−05 2.95E−02
TOMM5 1220.3 −0.26 0.06 −4.20 2.67E−05 3.09E−02
TRBV2 183.2 −0.76 0.18 −4.20 2.68E−05 3.09E−02
NKG7 13411.5 −0.80 0.20 −4.10 4.18E−05 4.22E−02
CLEC5A 417.1 0.72 0.18 4.09 4.28E−05 4.22E−02
TKTL1 319.1 −0.90 0.22 −4.09 4.33E−05 4.22E−02
RAB25 21.6 1.21 0.30 4.07 4.69E−05 4.34E−02
COL13A1 61.1 −1.39 0.34 −4.04 5.35E−05 4.71E−02
RBM11 82.6 0.68 0.17 3.96 7.55E−05 6.23E−02
AC008764.4 9.4 3.06 0.78 3.94 8.20E−05 6.23E−02
CKB 231.1 −0.87 0.22 −3.93 8.33E−05 6.23E−02
GNGT2 367.7 −0.44 0.11 −3.93 8.43E−05 6.23E−02
LAMC3 33.6 1.19 0.30 3.91 9.19E−05 6.40E−02
NEFL 189.0 0.90 0.23 3.90 9.44E−05 6.40E−02
ZNF154 506.7 0.69 0.18 3.90 9.69E−05 6.40E−02
C12orf75 1265.5 −0.43 0.11 −3.88 1.03E−04 6.40E−02
MSC-AS1 79.1 −1.20 0.31 −3.88 1.05E−04 6.40E−02
RPL39L 76.6 −0.90 0.23 −3.87 1.09E−04 6.40E−02
PPFIBP1 129.1 0.65 0.17 3.87 1.11E−04 6.40E−02
ACOT7 284.8 −0.43 0.11 −3.85 1.18E−04 6.51E−02
CDKN1C 1312.3 −0.91 0.24 −3.84 1.21E−04 6.51E−02
CKS1B 292.4 −0.33 0.09 −3.84 1.25E−04 6.51E−02
LINC00174 418.7 0.45 0.12 3.83 1.28E−04 6.51E−02
PALM 9.6 −1.60 0.42 −3.83 1.30E−04 6.51E−02
CABP4 57.2 −0.81 0.21 −3.81 1.36E−04 6.63E−02
EFNA5 29.3 −1.30 0.34 −3.80 1.46E−04 6.92E−02
LYPD2 140.9 −1.25 0.33 −3.77 1.64E−04 7.57E−02
DRAXIN 171.1 −1.19 0.32 −3.76 1.73E−04 7.78E−02
B3GAT1 380.0 −1.29 0.35 −3.73 1.93E−04 8.17E−02
TPST2 4420.9 −0.30 0.08 −3.72 1.96E−04 8.17E−02
CROCC2 21.0 −1.41 0.38 −3.72 1.99E−04 8.17E−02
FCRL6 1356.3 −0.79 0.21 −3.72 2.01E−04 8.17E−02
AC026369.3 23.0 −1.28 0.34 −3.71 2.03E−04 8.17E−02
C19orf12 1194.0 −0.27 0.07 −3.69 2.24E−04 8.72E−02
S100B 576.5 −1.95 0.53 −3.69 2.26E−04 8.72E−02
GAS1 40.1 −1.22 0.33 −3.68 2.33E−04 8.80E−02
JAKMIP1 389.4 −0.81 0.22 −3.67 2.40E−04 8.88E−02
LINC02345 34.2 −1.17 0.32 −3.65 2.61E−04 9.45E−02
GPR153 141.6 −0.92 0.25 −3.63 2.81E−04 9.86E−02
S1PR5 2888.0 −0.72 0.20 −3.63 2.87E−04 9.86E−02
MIR3150BHG 23.3 1.37 0.38 3.63 2.88E−04 9.86E−02
TABLE 17
SE_WBC_FXSvSTD
GeneID chr strand exonStart_0base exonEnd PValue FDR IncLevelDifference
PARP6 chr15 − 72253949 72254070 4.13E−05 0.0047705 −0.261
NCALD chr8 − 101887140 101887227 3.53E−07 9.83E−05 −0.259
PACRGL chr4 + 20709682 20709773 1.40E−11 1.94E−08 −0.256
TCF7 chr5 + 134144796 134144869 0.0003658 0.02606201 −0.233
ADAM15 chr1 + 155061903 155062117 0.0005209 0.03425292 −0.214
LAIR2 chr19 + 54509034 54509085 3.42E−05 0.00409749 −0.213
XPNPEP3 chr22 + 40860677 40860793 9.18E−05 0.00887286 −0.212
ADAM15 chr1 + 155061903 155061975 0.00013706 0.01211011 −0.209
POLR2J3 chr7 − 102543524 102543661 0.00010433 0.00977206 −0.201
POLR2J3 chr7 − 102543524 102543697 0.00033231 0.02419548 −0.191
LINC00937 chr12 − 8370212 8370429 0.00027255 0.02051526 −0.189
WARS1 chr14 − 100374135 100374244 0.00017291 0.01455804 −0.189
ADAM15 chr1 + 155061417 155061489 3.33E−05 0.00400639 −0.188
ADAM15 chr1 + 155061414 155061489 3.65E−05 0.00430797 −0.185
AL135818.1 chr14 + 91247489 91247659 8.11E−07 0.00019871 −0.182
AC092070.2 chr19 + 53200623 53200703 5.18E−06 0.00087303 −0.18
TRPT1 chr11 − 64224099 64224162 0.0001713 0.01445306 −0.18
DST chr6 − 56468981 56468999 5.43E−05 0.00585469 −0.177
WARS1 chr14 − 100374135 100374265 4.29E−05 0.00488853 −0.177
MIR4435-2HG chr2 − 111239801 111239996 2.76E−08 1.26E−05 −0.177
LRRFIP1 chr2 + 237739231 237739309 0.00012458 0.01126227 −0.167
ADCY10P1 chr6 + 41132874 41133000 0.00040264 0.02818434 −0.161
RNF19A chr8 − 100300527 100300651 0.00036871 0.02622929 −0.159
DRAM2 chr1 − 111139587 111139711 4.04E−05 0.00467528 −0.157
TRPV2 chr17 + 16433573 16433698 0.00020503 0.01646975 −0.156
CAST chr5 + 96740744 96740783 5.98E−11 6.79E−08 −0.154
C11orf80 chr11 + 66756352 66756505 0.00032101 0.0235863 −0.154
ZNF266 chr19 − 9433667 9433786 4.78E−05 0.00534689 −0.154
HMOX2 chr16 + 4483636 4483738 1.82E−05 0.00248133 −0.152
JPX chrX + 73997040 73997166 2.91E−13 6.92E−10 −0.152
ZNF266 chr19 − 9433667 9433783 0.00010286 0.00967682 −0.15
DPM1 chr20 − 50941128 50941209 4.29E−08 1.78E−05 −0.144
FRG1 chr4 + 189955036 189955151 9.86E−05 0.00935286 −0.141
FRG1 chr4 + 189953067 189953125 0.00049781 0.03310633 −0.14
COPS3 chr17 − 17261599 17261692 4.89E−05 0.0054405 −0.136
METTL8 chr2 − 171330558 171330616 1.60E−08 7.78E−06 −0.135
FCRLA chr1 + 161710474 161710492 0.00043161 0.02964294 −0.134
WARS1 chr14 − 100374135 100374244 6.02E−09 3.43E−06 −0.134
WARS1 chr14 − 100374135 100374265 3.15E−09 1.91E−06 −0.131
PMS2CL chr7 + 6733398 6733527 0.00072483 0.04450076 −0.128
MUC20-OT1 chr3 + 195663623 195663767 5.26E−05 0.00572117 −0.128
ZNF273 chr7 + 64918196 64918292 1.51E−07 5.06E−05 −0.127
NQO2 chr6 + 3003668 3003789 1.12E−05 0.00165072 −0.127
AC141586.1 chr16 + 2613959 2614068 3.03E−07 8.65E−05 −0.126
PNPO chr17 + 47945558 47945612 1.85E−05 0.0025123 −0.125
BFAR chr16 + 14649803 14649973 2.33E−07 7.10E−05 −0.12
GBAP1 chr1 − 155218387 155218479 1.00E−06 0.00023493 −0.119
RAB18 chr10 + 27531528 27531615 1.38E−06 0.00030182 −0.115
GPS1 chr17 + 82052255 82052459 0.00034465 0.02477726 −0.114
TAF5 chr10 + 103378234 103378550 2.32E−05 0.00299072 −0.11
HMOX2 chr16 + 4483636 4483754 3.00E−05 0.00368734 −0.109
PACRGL chr4 + 20712787 20712922 7.13E−12 1.09E−08 −0.109
IZUMO4 chr19 + 2097928 2098127 6.33E−10 4.73E−07 −0.109
ANKS3 chr16 − 4726978 4727177 1.48E−06 0.0003182 −0.106
SEPTIN2 chr2 + 241316421 241316540 3.83E−05 0.00448192 −0.106
YY1AP1 chr1 − 155680381 155680456 3.89E−07 0.00010641 −0.106
OFD1 chrX + 13752703 13753441 9.82E−06 0.00148129 −0.104
AC012184.3 chr16 − 70341939 70342099 1.57E−05 0.00217971 −0.102
SEPTIN2 chr2 + 241316421 241316575 0.00031701 0.02334237 −0.1
LAIR2 chr19 + 54507890 54508184 8.07E−12 1.20E−08 −0.099
SEPTIN2 chr2 + 241316421 241316555 0.00052281 0.03430146 −0.099
LDAH chr2 − 20739970 20740205 4.09E−05 0.00472452 −0.099
CDC42BPG chr11 − 64827685 64827783 3.34E−11 4.14E−08 −0.099
ZNF273 chr7 + 64918196 64918292 1.40E−07 4.80E−05 −0.098
VMP1 chr17 + 59834011 59834050 0.00046842 0.03154095 −0.096
ATP6AP1L chr5 + 82304933 82305481 0.00046338 0.03133037 −0.096
COMMD2 chr3 − 149750256 149750382 0.00060936 0.03880713 −0.095
PPRC1 chr10 + 102138878 102138980 6.73E−05 0.00694378 −0.095
RHBDF2 chr17 − 76487973 76488132 8.86E−06 0.0013551 −0.095
ZNF56 chr19 + 19786608 19786691 0.00049007 0.03267808 −0.095
SRSF4 chr1 − 29166728 29166912 9.13E−12 1.33E−08 −0.094
ZNF529-AS1 chr19 + 36594155 36594299 4.85E−05 0.00540113 −0.092
TNK2 chr3 − 195882444 195882527 0.00046703 0.03149965 −0.092
ANKS3 chr16 − 4726658 4726776 1.18E−06 0.00026688 −0.091
SUCO chr1 + 172585857 172585948 8.87E−05 0.00866587 −0.09
TBC1D19 chr4 + 26717932 26718017 2.91E−08 1.31E−05 −0.089
WARS1 chr14 − 100374135 100374179 3.29E−10 2.78E−07 −0.089
ITGB7 chr12 − 53201146 53201194 8.02E−06 0.0012518 −0.089
CYB5RL chr1 − 54190747 54190896 0.00010043 0.0094911 −0.088
WARS1 chr14 − 100374135 100374244 9.70E−12 1.40E−08 −0.086
IFI44L chr1 + 78627905 78628393 2.03E−05 0.00268837 −0.086
TGIF1 chr18 + 3450321 3450505 7.31E−05 0.0074397 −0.085
ZBTB25 chr14 − 64499440 64499563 2.44E−06 0.00047767 −0.084
FKRP chr19 + 46748514 46748621 0.00019209 0.01575417 −0.083
NSUN5P1 chr7 + 75414639 75414798 0.00080454 0.04836462 −0.082
ADAM15 chr1 + 155060762 155060832 4.27E−07 0.00011535 −0.082
PRKCQ-AS1 chr10 + 6615369 6615637 1.31E−12 2.48E−09 −0.082
TRPT1 chr11 − 64224099 64224210 3.63E−11 4.46E−08 −0.082
NCAPG2 chr7 − 158650831 158650972 4.67E−05 0.00523241 −0.081
IP6K2 chr3 − 48694458 48694525 0.00031741 0.02336111 −0.081
ALS2CL chr3 − 46683129 46683326 5.57E−06 0.00092703 −0.081
NFS1 chr20 − 35675044 35675202 3.47E−05 0.00414001 −0.08
LINC00174 chr7 − 66476258 66476327 1.41E−06 0.00030682 −0.08
CYRIB chr8 − 129948965 129949067 1.23E−07 4.28E−05 −0.079
CDC27 chr17 − 47171916 47172064 0.00075957 0.04618237 −0.079
ZNF202 chr11 − 123727475 123727595 0.00013216 0.01174517 −0.079
GOLGA2P5 chr12 − 100168451 100168633 1.97E−08 9.30E−06 −0.079
ZNF85 chr19 + 20944251 20944296 0.00018604 0.0153503 −0.079
FBXW8 chr12 + 116985205 116985402 1.98E−10 1.81E−07 −0.078
COA8 chr14 + 103571622 103571820 0.00045145 0.03068469 −0.078
NSRP1 chr17 + 30163066 30163162 7.97E−05 0.00795361 −0.078
KLRC4-KLRK1 chr12 − 10391834 10391891 7.17E−05 0.00732472 −0.077
OFD1 chrX + 13753367 13753441 3.23E−06 0.00059739 −0.075
FKRP chr19 + 46748514 46748884 0.00011155 0.01033948 −0.075
BCLAF3 chrX − 19929784 19929940 0.00060414 0.03851649 −0.075
SRPK2 chr7 − 105268805 105268869 1.22E−06 0.00027299 −0.073
WARS1 chr14 − 100374135 100374265 1.03E−13 2.84E−10 −0.073
HPCAL1 chr2 + 10426219 10426495 1.27E−06 0.00028331 −0.073
RXYLT1 chr12 + 63782540 63782704 0.00069902 0.04321791 −0.073
CARMIL1 chr6 + 25604811 25604893 0.00024006 0.01852197 −0.072
RAD51C chr17 + 58705877 58706022 9.33E−05 0.00897361 −0.072
HEATR6 chr17 − 60046024 60046099 3.33E−07 9.41E−05 −0.072
CROCC chr1 + 16950952 16951122 1.45E−08 7.20E−06 −0.071
AL732372.2 chr1 − 502861 502955 4.19E−06 0.00073262 −0.071
DTNB chr2 − 25607235 25607321 1.51E−05 0.00211344 −0.071
PLPP1 chr5 − 55475298 55475450 2.31E−05 0.00298281 −0.07
CTNS chr17 + 3647443 3647522 2.82E−06 0.00053717 −0.07
COP1 chr1 − 176175909 176176007 6.87E−05 0.00706358 −0.07
NEK3 chr13 − 52135728 52135863 2.07E−05 0.00273898 −0.07
POLA1 chrX + 24745417 24745542 0.00041351 0.028716 −0.068
LSM14B chr20 + 62126225 62126439 0.0001512 0.01303926 −0.068
CCDC18-AS1 chr1 − 93269682 93269758 0.00018251 0.01513776 −0.068
LYPLAL1-DT chr1 − 219156119 219156199 0.00057693 0.03713179 −0.068
SLC25A43 chrX + 119410189 119410362 1.91E−06 0.00039254 −0.067
BRAF chr7 − 140808236 140808316 2.75E−05 0.00342273 −0.067
STX3 chr11 + 59795601 59795712 5.00E−05 0.00551868 −0.067
PPFIA1 chr11 + 70350993 70351023 2.51E−05 0.00318434 −0.067
UBR2 chr6 + 42592150 42592229 9.35E−05 0.00897617 −0.066
SRP14-AS1 chr15 + 40060096 40060263 0.00014309 0.0124806 −0.065
ZBTB7B chr1 + 155010915 155011015 4.05E−10 3.31E−07 −0.065
BCLAF3 chrX − 19935808 19935898 0.00020359 0.01641398 −0.064
SFI1 chr22 + 31603743 31603819 8.00E−12 1.20E−08 −0.063
FKRP chr19 + 46748514 46748717 0.00019606 0.01598112 −0.063
STAG3L3 chr7 − 72999054 72999162 1.40E−05 0.00199305 −0.063
IMMP1L chr11 − 31473723 31473786 2.67E−11 3.43E−08 −0.063
PNPO chr17 + 47945860 47945989 3.41E−06 0.00062323 −0.063
BBS2 chr16 − 56500853 56500977 5.46E−05 0.0058751 −0.063
PIGT chr20 + 45418771 45418979 0.0006181 0.03923712 −0.062
PAAF1 chr11 + 73878782 73878819 1.82E−06 0.0003766 −0.062
NQO2 chr6 + 3003668 3003789 5.29E−10 4.15E−07 −0.062
NT5DC2 chr3 − 52524816 52524881 1.97E−05 0.00263448 −0.062
PRKCQ-AS1 chr10 + 6608347 6608408 1.22E−12 2.38E−09 −0.062
OSBPL5 chr11 − 3120543 3120624 0.00038382 0.0271477 −0.062
MAPKAPK5 chr12 + 111868752 111868861 1.45E−05 0.00204087 −0.062
ITGAE chr17 − 3723287 3723383 1.81E−07 5.85E−05 −0.062
PCBP1-AS1 chr2 − 70081369 70081490 7.56E−06 0.00119125 −0.062
FAM229B chr6 + 112097040 112097201 1.81E−05 0.00246972 −0.061
ZSCAN25 chr7 + 99621372 99621574 9.90E−06 0.00149139 −0.061
OBSCN chr1 + 228299881 228300145 2.61E−05 0.00329903 −0.061
HDAC10 chr22 − 50247691 50247776 1.96E−05 0.00262346 −0.061
ACAD10 chr12 + 111727961 111728143 7.99E−08 2.98E−05 −0.061
JPX chrX + 73994839 73994961 2.10E−11 2.78E−08 −0.061
NUBP2 chr16 + 1786756 1786955 0.00073545 0.04498019 −0.061
FRG1BP chr20 + 30391196 30391308 0.00043121 0.02962953 −0.06
PDPR chr16 + 70130422 70130544 0.0007527 0.04582763 −0.06
RAB3IP chr12 + 69800208 69800332 2.98E−10 2.61E−07 −0.06
HEATR3 chr16 + 50066366 50066539 4.11E−07 0.00011123 −0.06
LSM14B chr20 + 62126225 62126439 2.59E−05 0.00327671 −0.058
POGLUT3 chr11 − 108482005 108482222 2.48E−05 0.00315388 −0.058
TPP2 chr13 + 102651338 102651397 2.08E−07 6.48E−05 −0.058
TRPM7 chr15 − 50578558 50578664 2.19E−05 0.00287558 −0.058
NDUFAF5 chr20 + 13794837 13794941 0.00013562 0.01199553 −0.057
WARS1 chr14 − 100374135 100374220 1.07E−10 1.08E−07 −0.057
RAB3IP chr12 + 69800208 69800337 3.88E−10 3.20E−07 −0.057
LARGE2 chr11 + 45928176 45928372 1.94E−06 0.00039701 −0.057
DPAGT1 chr11 − 119097854 119097925 0.00058182 0.0373643 −0.057
DUSP16 chr12 − 12500518 12500682 8.11E−08 3.01E−05 −0.057
KDM3B chr5 + 138386288 138386621 1.42E−05 0.00201007 −0.056
KMT2B chr19 + 35719468 35719541 3.80E−06 0.00067495 −0.056
NQO2 chr6 + 3004494 3004651 3.73E−07 0.00010259 −0.056
COA1 chr7 − 43650611 43650712 1.57E−14 5.19E−11 −0.056
GARS1-DT chr7 − 30551317 30551395 5.76E−06 0.00095019 −0.055
TPP2 chr13 + 102651358 102651397 0.00039893 0.02799129 −0.055
NMRK1 chr9 − 75069741 75069813 0 0 −0.055
MMEL1 chr1 − 2591931 2592027 8.06E−06 0.00125569 −0.055
ABCA11P chr4 − 437445 437511 0.00022197 0.01743278 −0.055
UPP1 chr7 + 48103296 48103411 2.29E−07 7.03E−05 −0.055
PHF1 chr6 + 33414954 33415081 4.31E−06 0.00075119 −0.055
TMEM218 chr11 − 125110643 125110746 3.02E−05 0.00369849 −0.055
MAP7D3 chrX − 136231543 136232097 3.35E−07 9.45E−05 −0.054
ZNF653 chr19 − 11500677 11500815 0.00045619 0.0309349 −0.054
AC010175.1 chr12 + 9247580 9247677 0.00035803 0.02558081 −0.054
DHODH chr16 + 72022361 72022475 8.17E−07 0.00019983 −0.054
TUBGCP6 chr22 − 50220191 50221874 6.63E−05 0.00686126 −0.054
TUBGCP6 chr22 − 50221274 50221874 0.00012187 0.01108574 −0.054
TTLL3 chr3 + 9817644 9817759 4.18E−06 0.00073262 −0.053
TEX10 chr9 − 100308499 100308681 2.70E−07 7.88E−05 −0.053
SPATS2 chr12 + 49486249 49486348 0.00012318 0.01117043 −0.053
ZNF76 chr6 + 35293750 35293915 0.00082746 0.04947171 −0.052
FKRP chr19 + 46748514 46748665 6.12E−06 0.0009992 −0.052
SAR1B chr5 − 134632076 134632195 3.18E−05 0.0038478 −0.052
ZEB2 chr2 − 144398300 144400270 3.78E−05 0.00444011 −0.052
COA1 chr7 − 43657215 43657269 0.00051797 0.03412416 −0.052
SLC44A2 chr19 + 10635430 10635515 0.00027587 0.02071182 −0.052
BCLAF3 chrX − 19935808 19935898 0.00011236 0.01039656 −0.052
TRMT2B chrX − 101041316 101041371 1.46E−06 0.00031309 −0.052
PITPNM2 chr12 − 123013827 123014042 0.00064725 0.04070432 −0.052
IFT52 chr20 + 43605001 43605216 0.00072713 0.04462656 −0.051
P4HA1 chr10 − 73044980 73045051 0.0001243 0.01124914 −0.051
NUTM2A-AS1 chr10 − 87241181 87245855 1.07E−06 0.00024572 −0.051
SIGIRR chr11 − 406875 406993 9.72E−05 0.00925338 −0.051
ACAD10 chr12 + 111702161 111702310 0.00018525 0.01530743 −0.051
ZMYM5 chr13 − 19837655 19837821 1.92E−08 9.13E−06 −0.051
AC243960.1 chr19 + 41551179 41551494 0.00041006 0.02852178 −0.051
ZMYM3 chrX − 71251177 71251250 1.94E−07 6.19E−05 −0.05
VNN2 chr6 − 132752672 132752749 0.00014537 0.01265431 −0.05
SERINC5 chr5 − 80169334 80169546 0.00037287 0.02649055 −0.05
POGLUT3 chr11 − 108479300 108479495 1.75E−06 0.00036475 −0.05
LAIR1 chr19 − 54364294 54364486 0.00073871 0.04510092 −0.05
BAZ2A chr12 − 56615013 56615128 0.00048423 0.03232551 −0.05
FCGRT chr19 + 49525456 49525561 0.00035582 0.02549548 −0.05
GGA1 chr22 + 37613118 37613191 8.63E−07 0.0002093 0.05
TMEM161B- chr5 + 88285743 88285851 0.00038272 0.02708038 0.05
AS1
KRIT1 chr7 − 92245426 92245595 2.69E−06 0.00051737 0.05
SAMD4B chr19 + 39351816 39352374 2.97E−05 0.00365176 0.05
FRG1CP chr20 − 28590556 28590614 2.46E−06 0.00048012 0.05
ACADVL chr17 + 7220463 7220529 0.00031328 0.02311622 0.05
KIF27 chr9 − 83880296 83880494 2.29E−05 0.00296755 0.05
NBPF12 chr1 + 146989573 146989746 1.43E−10 1.41E−07 0.05
NUP62 chr19 − 49927693 49927848 0.00014724 0.0127722 0.05
CEP295 chr11 + 93724253 93724375 1.70E−12 3.16E−09 0.05
RHNO1 chr12 + 2885282 2885534 0.00019107 0.01569934 0.05
FANCI chr15 + 89293832 89293997 0.00021701 0.01717253 0.05
RMDN1 chr8 − 86474819 86474914 5.68E−10 4.36E−07 0.05
UBA52 chr19 + 18573292 18573403 0.00068996 0.04276343 0.05
ELF4 chrX − 130081255 130081312 0.00056335 0.03639137 0.05
MVK chr12 + 109579801 109579946 9.67E−05 0.00923448 0.051
WASHC2A chr10 + 50127159 50127222 4.22E−05 0.00483907 0.051
TMEM79 chr1 + 156285183 156285267 4.51E−05 0.00510788 0.051
BANP chr16 + 88027482 88027650 1.03E−10 1.05E−07 0.051
EBLN3P chr9 + 37080341 37080536 5.97E−06 0.00098069 0.051
ITGB3BP chr1 − 63510064 63510181 6.66E−16 2.79E−12 0.051
TMEM267 chr5 − 43453657 43454043 0.00076186 0.04625754 0.051
SLC25A37 chr8 + 23543087 23543211 0.0003385 0.02448361 0.051
SERPING1 chr11 + 57599863 57600377 0.00046854 0.03154095 0.051
AC087632.2 chr15 − 64207508 64207594 0.00073729 0.0450565 0.051
TGFB3 chr14 − 75960268 75960386 3.21E−05 0.0038857 0.051
TPT1-AS1 chr13 + 45383759 45383838 9.55E−06 0.00144378 0.052
LGMN chr14 − 92706482 92706653 4.01E−06 0.0007065 0.052
INO80C chr18 − 35479299 35479411 1.46E−09 9.93E−07 0.052
INO80C chr18 − 35480452 35480563 1.92E−05 0.00258784 0.052
TAF11 chr6 − 34879966 34880063 0.00045678 0.03096276 0.052
ATRIP chr3 + 48461360 48461445 0.00076043 0.04619117 0.052
NCOR2 chr12 − 124457105 124457162 5.36E−05 0.00579242 0.052
GTDC1 chr2 − 143952772 143952843 0.00073332 0.04488078 0.052
CPVL chr7 − 29066022 29066121 1.65E−06 0.00034657 0.052
PVT1 chr8 + 128070159 128070272 2.50E−07 7.46E−05 0.052
RNPS1 chr16 − 2267174 2267218 3.71E−06 0.0006642 0.052
A1BG-AS1 chr19 + 58353320 58353474 1.29E−06 0.00028542 0.052
PCBP1-AS1 chr2 − 70053730 70053792 0.00013037 0.01163059 0.052
CAMLG chr5 + 134741062 134741523 1.57E−06 0.00033148 0.053
TMBIM1 chr2 − 218285762 218285938 0.00058267 0.03740563 0.053
SLC15A2 chr3 + 121940383 121940488 3.62E−07 0.00010052 0.053
DENND4C chr9 + 19371755 19371820 8.89E−07 0.00021467 0.053
MAP3K20 chr2 + 173090997 173091190 2.15E−14 6.53E−11 0.053
RAB4A chr1 + 229288728 229288843 0.00041343 0.028716 0.053
NOD2 chr16 + 50707854 50707960 8.66E−15 3.11E−11 0.053
ERMARD chr6 + 169753943 169754032 3.14E−10 2.68E−07 0.054
ZNF354B chr5 + 178885613 178885737 4.82E−11 5.72E−08 0.054
NOTCH2 chr1 − 119948413 119948566 2.89E−12 4.93E−09 0.054
IP6K2 chr3 − 48715314 48715527 0.00065065 0.04087433 0.054
HLTF chr3 − 149041489 149041668 4.24E−05 0.00485771 0.054
TRAF3IP2-AS1 chr6 + 111574620 111574802 0.00038608 0.02727479 0.054
CCNL1 chr3 − 157157010 157157083 0.00057255 0.03689057 0.054
SYTL2 chr11 − 85714412 85714507 4.65E−05 0.00522027 0.054
DGUOK chr2 + 73938909 73939022 0.00059549 0.0380615 0.054
AGPAT5 chr8 + 6747669 6747828 0.0001124 0.01039656 0.055
VNN2 chr6 − 132760631 132760803 0.00021126 0.01683401 0.055
R3HCC1L chr10 + 98162882 98162975 9.11E−07 0.00021858 0.055
KIF27 chr9 − 83859155 83859371 3.06E−06 0.00057281 0.055
LINC00963 chr9 + 129493415 129493595 5.11E−05 0.00560086 0.055
JAK3 chr19 − 17839179 17839293 0.00046688 0.03149965 0.055
PPP4R1L chr20 − 58236153 58236274 9.49E−07 0.00022605 0.055
HM13 chr20 + 31567639 31567740 3.04E−05 0.00371772 0.055
HM13 chr20 + 31567639 31567806 0.00024524 0.01881368 0.055
GMFG chr19 − 39335260 39335310 7.40E−07 0.0001842 0.055
GGA1 chr22 + 37613023 37613191 1.38E−08 6.96E−06 0.056
CCM2 chr7 + 45070093 45070168 0.0002009 0.0162487 0.056
LY96 chr8 + 74004795 74004885 2.58E−07 7.66E−05 0.056
EIF4G3 chr1 − 21002712 21002808 4.69E−13 1.03E−09 0.056
SNX25 chr4 + 185258847 185259064 2.92E−06 0.00055518 0.056
METTL15 chr11 + 28122141 28122180 2.46E−06 0.00048012 0.056
CEP290 chr12 − 88054339 88054413 0.00028011 0.02100352 0.056
MAP4 chr3 − 47867245 47867338 1.96E−05 0.00262346 0.056
DPEP2 chr16 − 67992949 67993257 1.30E−05 0.00187949 0.056
TCEA3 chr1 − 23408663 23408726 1.82E−09 1.21E−06 0.057
ST6GALNAC4 chr9 − 127909950 127910528 1.60E−08 7.79E−06 0.057
CASP5 chr11 − 105003273 105003383 0.00012589 0.01134592 0.057
DLGAP4 chr20 + 36465264 36465367 2.58E−08 1.18E−05 0.057
RBIS chr8 − 85219235 85219360 3.77E−12 6.29E−09 0.057
LUCAT1 chr5 − 91303872 91303971 4.81E−05 0.0053638 0.057
PSTK chr10 + 122982732 122983024 1.29E−10 1.27E−07 0.057
GLT1D1 chr12 + 128914932 128914989 3.25E−05 0.00392457 0.057
GTF2I chr7 + 74744138 74744250 7.66E−05 0.00771126 0.057
NRDE2 chr14 − 90317703 90317820 3.30E−06 0.00060518 0.057
ST3GAL2 chr16 − 70400695 70401094 1.71E−05 0.00235683 0.057
SNAP23 chr15 + 42529674 42529819 7.93E−05 0.00792063 0.057
AC138894.1 chr16 − 28491481 28491513 0.00033205 0.02418896 0.057
LMAN2L chr2 − 96733518 96733601 1.71E−05 0.00235722 0.057
CERS4 chr19 + 8257878 8257985 0.0001142 0.01051884 0.057
PGAP2 chr11 + 3822908 3822993 0.00024356 0.0187041 0.058
SLC12A2 chr5 + 128177104 128177152 1.89E−05 0.00255504 0.058
CAMK4 chr5 + 111376859 111376942 1.77E−05 0.0024254 0.059
ABRAXAS1 chr4 − 83470202 83470396 3.64E−05 0.00429266 0.059
FCRL2 chr1 − 157770408 157770666 3.04E−10 2.63E−07 0.059
TANGO2 chr22 + 20061529 20061683 0.00041414 0.02874869 0.059
GGCT chr7 − 30500535 30500681 0.00041456 0.02876643 0.059
AP001781.2 chr11 − 111876480 111876639 7.12E−08 2.70E−05 0.059
NOD2 chr16 + 50716890 50716974 9.32E−05 0.00897361 0.059
FYN chr6 − 111754433 111754677 2.00E−05 0.00265702 0.059
CYBC1 chr17 − 82449430 82449956 0.00083258 0.04972718 0.059
CCDC191 chr3 − 114046590 114046732 0.00033287 0.0242138 0.059
ABHD12 chr20 − 25314924 25314970 5.56E−13 1.15E−09 0.06
FOPNL chr16 − 15873490 15873627 0.00081018 0.04858225 0.06
NEXN chr1 + 77935822 77936044 6.34E−09 3.58E−06 0.06
HFE chr6 + 26090840 26091104 3.03E−09 1.85E−06 0.06
TRMT2B chrX − 101041316 101041371 2.02E−08 9.45E−06 0.06
ABCD4 chr14 − 74299547 74299675 0.00012991 0.0116016 0.06
AC243960.1 chr19 + 41553705 41553746 1.76E−07 5.74E−05 0.06
PSMG4 chr6 + 3264173 3264325 1.27E−13 3.44E−10 0.061
IKBKG chrX + 154560406 154560559 4.93E−08 2.01E−05 0.061
TRMT61B chr2 − 28852407 28852499 6.76E−09 3.78E−06 0.061
IGHG3 chr14 − 105770292 105770337 5.40E−11 6.16E−08 0.061
ING3 chr7 + 120964741 120964838 0.00069568 0.04302677 0.061
RPL32P3 chr3 − 129396216 129396420 0.00027031 0.02037313 0.061
ABHD14A- chr3 + 51988523 51988603 7.03E−07 0.00017643 0.061
ACY1
TBCD chr17 + 82909284 82909307 0.00017435 0.01463332 0.061
RPAIN chr17 + 5426235 5426299 0.00064222 0.04046014 0.061
SULT1A1 chr16 − 28609930 28610191 1.89E−09 1.24E−06 0.061
TCFL5 chr20 − 62857394 62857638 1.07E−05 0.0015881 0.062
TCF25 chr16 + 89893788 89893858 1.11E−16 5.28E−13 0.062
COX20 chr1 + 244841943 244842058 0.00042949 0.02952315 0.062
SERGEF chr11 − 18010074 18010139 1.95E−12 3.53E−09 0.062
KIAA2026 chr9 − 5910614 5910707 1.48E−07 5.01E−05 0.062
CD40 chr20 + 46121723 46121898 2.44E−10 2.19E−07 0.063
KIR2DL1 chr19 + 54780088 54780166 7.23E−06 0.00114802 0.063
GPR141 chr7 + 37709717 37709799 0.00012656 0.01138908 0.063
LRRC37B chr17 + 32027768 32027840 2.39E−07 7.24E−05 0.063
TMEM44-AS1 chr3 + 194589020 194589142 8.89E−05 0.00867794 0.063
TYSND1 chr10 − 70142667 70142853 1.98E−08 9.32E−06 0.063
FGR chr1 − 27621558 27621657 0.00027468 0.02064046 0.063
ZNF133 chr20 + 18305680 18305807 3.37E−08 1.47E−05 0.063
BCL2L13 chr22 + 17696140 17696210 3.41E−09 2.05E−06 0.064
PMS2 chr7 − 6005891 6006031 8.86E−06 0.0013551 0.064
ARHGAP19 chr10 − 97256317 97256404 4.64E−06 0.00079573 0.064
TRIM34 chr11 + 5642816 5642853 2.54E−07 7.57E−05 0.064
ZBTB8OS chr1 − 32634767 32634792 9.81E−07 0.00023146 0.064
RESF1 chr12 + 31980877 31985957 4.45E−09 2.59E−06 0.064
CHD4 chr12 − 6580581 6580679 1.97E−05 0.00263448 0.064
ZNF133 chr20 + 18305667 18305807 4.93E−08 2.01E−05 0.064
RBM23 chr14 − 22905605 22905659 1.87E−10 1.74E−07 0.064
PCBP1-AS1 chr2 − 70059642 70059680 0.00048609 0.03243737 0.064
TMEM116 chr12 − 111978735 111978787 0.00013785 0.0121498 0.065
PI4KB chr1 − 151324744 151324917 9.31E−07 0.00022272 0.065
SNRPA1 chr15 − 101291961 101292040 0.00015456 0.01326347 0.065
PCBP1-AS1 chr2 − 70053730 70053812 0.00067913 0.04228381 0.065
HMOX2 chr16 + 4483636 4483754 1.07E−07 3.79E−05 0.066
GMDS-DT chr6 + 2269697 2269799 2.75E−08 1.26E−05 0.066
IL18R1 chr2 + 102367824 102368068 0.00052261 0.03430141 0.066
UPB1 chr22 + 24523618 24523773 2.78E−06 0.00053081 0.067
ZNF138 chr7 + 64815575 64815653 6.47E−07 0.0001639 0.067
GATC chr12 + 120454932 120455030 1.41E−12 2.64E−09 0.067
PIK3C2B chr1 − 204433792 204433949 9.40E−05 0.00901632 0.067
UPF3A chr13 + 114286301 114286400 5.83E−07 0.00015145 0.067
ANGEL2 chr1 − 213013092 213013418 1.14E−06 0.00026008 0.067
KRIT1 chr7 − 92245426 92245574 5.06E−05 0.00556272 0.067
CHD4 chr12 − 6580581 6580699 4.43E−05 0.00502057 0.067
SRPK2 chr7 − 105117366 105117511 7.42E−07 0.00018426 0.068
EVA1C chr21 + 32457596 32457720 2.06E−06 0.00041493 0.068
ACCS chr11 + 44082064 44082192 3.48E−06 0.00063292 0.068
DDX60L chr4 − 168377727 168377843 0.00014501 0.01263489 0.069
RBIS chr8 − 85219235 85219363 3.62E−08 1.55E−05 0.069
N4BP2L2 chr13 − 32537005 32537027 0.00039412 0.02769757 0.069
PCBP1-AS1 chr2 − 70053730 70053815 0.00059604 0.03808323 0.07
ERICH6-AS1 chr3 + 150706926 150707171 9.04E−05 0.00878768 0.071
ATP5MC2 chr12 − 53669870 53670114 3.11E−05 0.00378606 0.071
SRP54-AS1 chr14 − 34963928 34964040 6.97E−09 3.85E−06 0.071
ZBTB1 chr14 + 64516599 64516751 7.89E−10 5.73E−07 0.071
DTNBP1 chr6 − 15651312 15651408 3.31E−05 0.00399223 0.072
FAM228B chr2 + 24139369 24139450 0.0002296 0.01792704 0.072
METTL6 chr3 − 15415497 15415583 2.01E−06 0.00040859 0.072
KPTN chr19 − 47483294 47483379 1.14E−12 2.25E−09 0.072
POLK chr5 + 75590343 75590440 1.54E−08 7.56E−06 0.072
PGS1 chr17 + 78392513 78392665 1.39E−05 0.00197384 0.072
RPRD1B chr20 + 38040434 38040564 6.21E−05 0.00651006 0.073
LINC00426 chr13 − 30367600 30367717 0.00015329 0.01317999 0.073
CD160 chr1 + 145730743 145731070 1.88E−06 0.00038822 0.073
TAF2 chr8 − 119801793 119802025 0.00021154 0.01683401 0.073
IL15RA chr10 − 5963742 5963841 0.00012622 0.01136434 0.073
ANXA11 chr10 − 80172806 80172869 5.72E−08 2.25E−05 0.073
RALGAPB chr20 + 38535085 38535207 1.10E−05 0.00162754 0.074
FAM13B chr5 − 138019880 138019977 0.00027015 0.02036945 0.074
KIAA1191 chr5 − 176359810 176359918 0.00024098 0.01856021 0.074
DPEP2 chr16 − 67991114 67991184 0.00021514 0.01706313 0.074
CD226 chr18 − 69873143 69873246 2.09E−09 1.36E−06 0.074
PTPRA chr20 + 2975214 2975241 0.00024877 0.01904312 0.075
ZNF75D chrX − 135291471 135291563 0.00037561 0.02663134 0.075
NABP1 chr2 + 191682491 191682595 2.46E−05 0.00313708 0.075
EME2 chr16 + 1774259 1774352 1.02E−07 3.66E−05 0.075
SNRNP70 chr19 + 49102113 49102185 0.00048055 0.0321037 0.075
TRPV2 chr17 + 16431783 16431850 0.00012972 0.01159338 0.076
PLBD1-AS1 chr12 + 14614521 14614570 0.00025283 0.01929505 0.076
UBE3B chr12 + 109529889 109530072 0.0004074 0.02842036 0.076
CEP68 chr2 + 65069398 65069801 4.26E−05 0.00486704 0.076
ABRAXAS1 chr4 − 83472221 83472288 0.0004238 0.02924008 0.077
NLRP6 chr11 + 280083 281839 0.00019803 0.01608321 0.077
RIDA chr8 − 98108645 98108768 0.00024359 0.0187041 0.077
UBE3B chr12 + 109481636 109481742 0.00033307 0.0242138 0.077
AC243960.1 chr19 + 41551179 41551494 1.83E−07 5.90E−05 0.077
DPY19L1 chr7 − 34957983 34958070 4.23E−05 0.00485388 0.078
CLEC4C chr12 − 7741420 7741531 0 0 0.078
MADD chr11 + 47273826 47273976 3.73E−08 1.59E−05 0.078
CBWD3 chr9 + 68266219 68266306 6.84E−05 0.00703795 0.078
ANP32A chr15 − 68784396 68784595 6.85E−08 2.64E−05 0.078
ENDOV chr17 + 80422205 80422245 1.11E−06 0.00025451 0.078
FCGRT chr19 + 49521694 49521813 3.73E−10 3.11E−07 0.078
RNF8 chr6 + 37374619 37374709 3.64E−06 0.00065582 0.079
TFB1M chr6 − 155298476 155298585 1.30E−08 6.59E−06 0.079
LONP2 chr16 + 48256609 48256741 9.13E−08 3.34E−05 0.079
TMEM161B- chr5 + 88283009 88283086 1.55E−11 2.10E−08 0.079
AS1
TMEM161B- chr5 + 88285743 88285851 4.76E−10 3.81E−07 0.079
AS1
POLK chr5 + 75547009 75547157 0.00014255 0.01245137 0.079
PCBP1-AS1 chr2 − 70053730 70053994 0.00034297 0.02468499 0.079
RAB3A chr19 − 18202512 18202855 1.38E−05 0.0019656 0.079
SLC37A3 chr7 − 140355667 140355764 4.06E−06 0.00071342 0.08
MIR762HG chr16 + 30888713 30888958 0.00074552 0.04546944 0.08
MRS2 chr6 + 24408407 24408444 1.21E−05 0.00176555 0.08
TXNDC11 chr16 − 11733981 11734079 9.01E−11 9.60E−08 0.08
LUCAT1 chr5 − 91313077 91313229 0.00013473 0.01192874 0.08
CERS5 chr12 − 50144768 50144969 4.45E−08 1.83E−05 0.08
INO80E chr16 + 30001211 30003013 0.00066614 0.04162435 0.081
LUCAT1 chr5 − 91312294 91313229 0.00012709 0.01141316 0.081
AC096887.1 chr3 − 53092368 53092618 5.55E−16 2.38E−12 0.081
IRAK3 chr12 + 66203710 66203893 0.00011632 0.01068068 0.081
SGCB chr4 − 52033430 52033640 1.65E−05 0.00228656 0.081
CEP41 chr7 − 130426645 130426759 0.00015201 0.0130958 0.082
MPC1 chr6 − 166366968 166367184 8.10E−05 0.00806148 0.082
PPP2R2D chr10 + 131940030 131940196 6.03E−10 4.54E−07 0.082
TOGARAM2 chr2 + 29022157 29022308 2.07E−06 0.0004182 0.082
SLC25A37 chr8 + 23543087 23543211 1.09E−07 3.84E−05 0.082
ERLIN1 chr10 − 100164003 100164095 1.49E−06 0.0003182 0.082
COQ5 chr12 − 120526456 120526546 2.19E−05 0.00287254 0.082
TAF1C chr16 − 84183071 84183149 0.00014808 0.01283276 0.082
SNRNP70 chr19 + 49102113 49103587 0.00039909 0.02799129 0.082
INTS7 chr1 − 211946606 211946705 5.71E−06 0.00094441 0.083
DSTYK chr1 − 205160113 205160270 8.50E−05 0.00838539 0.083
CD44 chr11 + 35196745 35196874 4.00E−15 1.53E−11 0.083
RPL5 chr1 + 92833388 92833458 0 0 0.084
CCDC138 chr2 + 108856793 108856970 0.00038746 0.02733931 0.084
RMND5B chr5 + 178131236 178131376 0.00051842 0.03414128 0.084
SLC66A2 chr18 − 79947266 79947341 0.0001841 0.01522639 0.084
MAK chr6 − 10830547 10830877 7.56E−09 4.13E−06 0.084
ABITRAM chr9 + 108939195 108939272 7.76E−05 0.00778989 0.084
AC000120.4 chr7 − 92244001 92244149 1.21E−07 4.24E−05 0.085
TAMM41 chr3 − 11830721 11830874 3.07E−05 0.00374074 0.085
SP140 chr2 + 230245862 230245940 0.00047899 0.03202374 0.085
STAMBP chr2 + 73870142 73870352 8.16E−08 3.02E−05 0.085
UBXN8 chr8 + 30754664 30754749 2.76E−09 1.71E−06 0.086
CHROMR chr2 + 178426365 178426505 0.00020583 0.0165108 0.086
FANCG chr9 − 35076970 35077101 3.72E−09 2.21E−06 0.086
FGR chr1 − 27623690 27623929 1.02E−06 0.00023778 0.086
DPEP2 chr16 − 67992063 67992193 4.27E−05 0.00487076 0.086
RALGAPB chr20 + 38535073 38535207 1.90E−05 0.00256257 0.087
C1orf162 chr1 + 111477333 111477428 5.66E−05 0.00604978 0.087
GOLGA2P5 chr12 − 100168451 100168633 8.10E−11 8.95E−08 0.087
GMFG chr19 − 39335434 39335554 0.00019532 0.01594451 0.087
AC147651.1 chr7 + 524079 524280 3.44E−05 0.00411258 0.088
IQCB1 chr3 − 121788283 121788432 1.08E−05 0.00160687 0.088
ERLIN1 chr10 − 100167347 100167406 7.06E−09 3.89E−06 0.088
ATOX1 chr5 − 151751703 151751779 7.38E−06 0.00116593 0.089
RIDA chr8 − 98108645 98108713 0.00041987 0.02908235 0.089
TSPAN5 chr4 − 98484398 98484598 2.50E−05 0.00316784 0.089
SNHG17 chr20 − 38422095 38422241 0.00082527 0.0493766 0.09
MVK chr12 + 109581394 109581550 0.00061365 0.03905218 0.09
PSME3IP1 chr16 − 57178501 57178852 2.40E−05 0.00308252 0.09
POLK chr5 + 75593877 75594049 3.06E−10 2.63E−07 0.091
WDR20 chr14 + 102208602 102209862 0.00010367 0.00973724 0.091
DDX31 chr9 − 132625663 132625745 2.64E−07 7.76E−05 0.092
POLD1 chr19 + 50395024 50395150 5.69E−06 0.00094098 0.093
CAST chr5 + 96726753 96726859 0.00042357 0.02924008 0.093
TM7SF2 chr11 + 65115313 65115390 0.00059335 0.03796218 0.093
NSRP1 chr17 + 30118079 30118173 0.00046935 0.03155949 0.093
FAM210A chr18 − 13671861 13671973 6.79E−05 0.00699038 0.093
MYL5 chr4 + 677921 678029 5.32E−07 0.00013988 0.094
INO80C chr18 − 35487385 35487823 2.87E−11 3.64E−08 0.094
SIMC1 chr5 + 176289653 176290955 3.16E−05 0.00383582 0.094
ABHD16A chr6 − 31702073 31702130 0.0005242 0.03436691 0.095
DAP3 chr1 + 155721516 155721618 2.29E−14 6.82E−11 0.095
ANKRD26 chr10 − 27005622 27005723 3.57E−05 0.00424836 0.096
ADCY10P1 chr6 + 41118128 41118184 0.00035189 0.02525519 0.096
ADAP2 chr17 + 30926826 30926918 0.00024331 0.0187041 0.096
RPL5 chr1 + 92833544 92833660 2.35E−12 4.14E−09 0.097
ZCWPW1 chr7 − 100408538 100408659 3.34E−12 5.64E−09 0.097
SUSD3 chr9 + 93077845 93077993 1.05E−05 0.00157203 0.097
CHROMR chr2 + 178426365 178426680 0.00040373 0.02824711 0.097
TMEM126A chr11 + 85650248 85650341 6.70E−05 0.00692502 0.097
ZFP1 chr16 + 75166769 75166913 8.78E−08 3.22E−05 0.097
ZNF195 chr11 − 3369356 3369502 0.00021825 0.01723225 0.099
FPR2 chr19 + 51763361 51763517 2.85E−07 8.23E−05 0.1
DCLRE1C chr10 − 14936537 14936593 1.62E−07 5.37E−05 0.1
POU6F1 chr12 − 51206788 51206883 0.00031273 0.02310465 0.1
RPF2 chr6 + 110988987 110989065 0.00017936 0.01491853 0.102
MTSS1 chr8 − 124557680 124557875 0.00019476 0.01590625 0.102
TOP1MT chr8 − 143334107 143334285 5.37E−11 6.16E−08 0.102
CPVL chr7 − 29071772 29071904 6.61E−07 0.00016671 0.102
PTPA chr9 + 129127963 129128068 7.41E−05 0.00751031 0.102
PANK2 chr20 + 3916926 3917050 0.00028416 0.02126905 0.104
RGS18 chr1 + 192161452 192161487 3.98E−12 6.55E−09 0.104
CKLF chr16 + 66563071 66563217 0.00060251 0.03842654 0.105
PAK1 chr11 − 77397026 77397093 2.40E−05 0.00308189 0.105
HM13 chr20 + 31548676 31548793 8.18E−08 3.02E−05 0.106
LINC01934 chr2 + 181354207 181354343 1.49E−06 0.00031858 0.107
BBOF1 chr14 + 74049701 74050195 1.99E−06 0.00040514 0.108
BMPR2 chr2 + 202555251 202556531 0 0 0.108
AF117829.1 chr8 − 89725517 89725641 6.29E−05 0.00658311 0.109
THTPA chr14 + 23556742 23557304 0.00023326 0.01811627 0.11
C11orf80 chr11 + 66762078 66762450 0.0006439 0.04054371 0.11
UBL7 chr15 − 74451435 74451520 4.13E−05 0.00476553 0.11
TRIM5 chr11 − 5665168 5665395 8.80E−05 0.00861499 0.11
DICER1-AS1 chr14 + 95158875 95159035 5.53E−08 2.20E−05 0.11
AC009022.1 chr16 − 69990596 69990683 5.88E−06 0.00096664 0.11
POLR2J3 chr7 − 102545302 102545420 4.56E−05 0.00515092 0.111
MATR3 chr5 + 139279934 139280058 1.83E−07 5.90E−05 0.111
CBWD3 chr9 + 68269599 68269722 2.16E−12 3.83E−09 0.112
POU6F1 chr12 − 51206788 51206947 2.80E−05 0.00347364 0.113
TYSND1 chr10 − 70143841 70143972 9.39E−06 0.00142387 0.113
BBOF1 chr14 + 74049701 74050195 8.37E−11 9.09E−08 0.114
NBR2 chr17 + 43132598 43132723 7.30E−07 0.00018223 0.114
CCM2 chr7 + 45071749 45071872 0.0005479 0.03553924 0.115
MAP3K8 chr10 + 30437175 30437406 4.96E−05 0.00548092 0.117
AC008035.1 chr12 + 46571255 46571412 5.89E−07 0.00015221 0.117
LDLRAD4 chr18 + 13484036 13484119 0.00071613 0.04404337 0.117
PSMG4 chr6 + 3264208 3264325 5.52E−13 1.15E−09 0.119
ANAPC10 chr4 − 144999256 144999294 0.00053917 0.03508711 0.12
ZMYM1 chr1 + 35095818 35095891 0.00016202 0.01381607 0.122
ADCY10P1 chr6 + 41138608 41138726 3.48E−05 0.00414421 0.124
TCFL5 chr20 − 62859363 62859526 2.67E−07 7.83E−05 0.126
POLL chr10 − 101585315 101585478 0.00015474 0.0132661 0.127
DPH7 chr9 − 137576308 137576402 0.00034008 0.02454786 0.127
MOK chr14 − 102231706 102231821 2.84E−08 1.28E−05 0.128
MECP2 chrX − 154056940 154057254 0.00057966 0.03725292 0.129
HLA-DPA1 chr6 − 33069018 33069300 8.76E−09 4.64E−06 0.131
HM13 chr20 + 31548379 31548793 5.44E−10 4.24E−07 0.131
MVK chr12 + 109579801 109579946 5.42E−05 0.0058498 0.133
ZBTB8OS chr1 − 32634767 32634792 0.00069151 0.04281367 0.133
DOCK2 chr5 + 170075946 170076084 1.42E−07 4.85E−05 0.136
WBP1 chr2 + 74458831 74459117 5.28E−05 0.00573478 0.137
VMP1 chr17 + 59764970 59765138 1.93E−06 0.00039672 0.138
MYOM1 chr18 − 3135546 3135730 2.96E−07 8.46E−05 0.139
FYB1 chr5 − 39212677 39213017 0.00024024 0.0185248 0.14
EVA1C chr21 + 32457596 32457720 0.00074596 0.04547061 0.146
AC093157.1 chr1 + 101072659 101072830 0.0003899 0.02748942 0.148
TRAF3IP1 chr2 + 238333959 238334035 1.10E−05 0.00162144 0.149
SNHG17 chr20 − 38422091 38422241 1.43E−05 0.00202187 0.151
YWHAH chr22 + 31945499 31945678 0.00019982 0.01618391 0.151
ARMCX5- chrX + 102639399 102639533 0 0 0.152
GPRASP2
AC009022.1 chr16 − 69992910 69993248 8.12E−05 0.00807253 0.152
ZNF232 chr17 − 5111075 5111219 0.00033549 0.02434619 0.154
CENPN chr16 + 81022596 81022652 0.0006022 0.03842064 0.155
WBP1 chr2 + 74458831 74458919 6.08E−05 0.00641584 0.157
ITGB3BP chr1 − 63510064 63510181 2.53E−10 2.26E−07 0.157
MPV17 chr2 − 27317077 27317234 2.53E−08 1.17E−05 0.157
MTIF3 chr13 − 27441016 27441077 2.66E−15 1.04E−11 0.16
LRRC23 chr12 + 6909889 6910026 0.00023432 0.01816614 0.16
TMEM143 chr19 − 48360071 48360176 1.29E−06 0.00028542 0.16
NEIL2 chr8 + 11770173 11770335 0.00071612 0.04404337 0.168
TMEM161B- chr5 + 88283009 88283086 7.14E−06 0.00113677 0.168
AS1
INTS7 chr1 − 211946606 211946645 0.0002666 0.02016249 0.17
TRAF3IP2-AS1 chr6 + 111574620 111574802 0.00055747 0.03605107 0.174
GOLGA8A chr15 − 34435382 34435471 0.00012208 0.01109905 0.174
BBS9 chr7 + 33352858 33352873 9.71E−06 0.00146679 0.175
PPIEL chr1 − 39523806 39523896 0.00050728 0.03362161 0.177
TUBGCP4 chr15 + 43399111 43399174 3.59E−05 0.00426133 0.177
AC060780.1 chr17 − 43159422 43159727 0.00051785 0.03412416 0.18
ECHDC2 chr1 − 52899173 52899224 1.41E−06 0.00030698 0.182
UROS chr10 − 125789282 125789363 0.00043473 0.02978484 0.182
MAFG chr17 − 81923352 81923416 6.25E−07 0.00015941 0.186
GIPR chr19 + 45671284 45671392 0.00031083 0.02297403 0.186
HCLS1 chr3 − 121636433 121636489 0 0 0.191
AC016727.1 chr2 + 61480299 61480583 0.00021804 0.01723082 0.192
SNHG17 chr20 − 38422091 38422241 0.00033397 0.02426582 0.195
AC022137.3 chr19 + 53446226 53446337 0.00020113 0.01625268 0.195
CWF19L1 chr10 − 100260217 100260319 0.00023318 0.01811627 0.201
LRRC23 chr12 + 6912729 6913027 7.97E−06 0.00124443 0.208
TMEM143 chr19 − 48360071 48360183 3.32E−05 0.0039934 0.209
VNN2 chr6 − 132760631 132760803 3.87E−05 0.0045206 0.214
AAMDC chr11 + 77841018 77841060 4.39E−07 0.00011773 0.22
TPRKB chr2 − 73734527 73734588 4.40E−05 0.00499846 0.228
FCHSD1 chr5 − 141642396 141642503 2.48E−06 0.00048344 0.246
PYROXD2 chr10 − 98388353 98388508 0.00010894 0.01012971 0.249
STRA6LP chr9 + 97347313 97347666 1.73E−08 8.32E−06 0.255
SERPINB9P1 chr6 − 2857910 2857991 0.00045903 0.03110341 0.266
AC245100.4 chr1 + 148424062 148424189 3.71E−07 0.0001022 0.268
PGAP3 chr17 − 39676613 39676755 2.22E−16 1.00E−12 0.319
TABLE 18
MXE_FXSvsTD
GeneID chr strand 1stExonStart_0base 1stExonEnd 2ndExonStart_0base 2ndExonEnd
CR1 chr1 + 207526752 207526929 207545307 207545484
PIGL chr17 + 16313546 16313614 16316680 16316712
XPNPEP3 chr22 + 40870047 40870139 40881769 40882177
MAPKBP1 chr15 + 41813620 41813781 41815258 41815405
TBC1D12 chr10 + 94522343 94522453 94531201 94531460
AC004593.2 chr7 + 29146848 29146960 29354624 29354663
AC016831.6 chr7 − 130912109 130912152 130945719 130945835
WDR60 chr7 + 158905988 158906091 158911549 158911679
ZNF720 chr16 + 31723257 31723353 31753765 31753900
MYO15B chr17 + 75603031 75603077 75605863 75606021
HSD17B3 chr9 − 96252802 96252910 96254867 96254943
WHAMMP3 chr15 + 22674420 22674586 22676804 22676934
AL392172.1 chr1 + 222835118 222835215 222836995 222837066
ATXN2 chr12 − 111456028 111456256 111464661 111464715
AL356481.1 chr9 − 128536826 128536955 128543378 128543684
PDE8A chr15 + 85109052 85109130 85113376 85113447
ZNF266 chr19 − 9433667 9433786 9434797 9434859
AL162258.1 chr1 − 153627482 153627598 153631010 153631078
CAMKK1 chr17 − 3882527 3882564 3883041 3883175
PPFIA1 chr11 + 70349922 70350039 70350993 70351023
ZNF266 chr19 − 9434074 9434235 9434797 9434859
CFAP70 chr10 − 73277239 73277361 73278178 73278337
ACCS chr11 + 44071255 44071315 44073446 44073517
ATF7IP2 chr16 + 10473922 10473989 10480878 10480964
NEIL2 chr8 + 11771445 11771590 11779597 11779950
TAF4 chr20 − 62006509 62006758 62007546 62007636
PNPT1 chr2 − 55666990 55667093 55671318 55671376
HLA-DRB5 chr6 − 32519369 32519651 32521904 32522174
DDX60L chr4 − 168391539 168391644 168395958 168396124
YAF2 chr12 − 42172139 42172209 42235613 42235755
SP140 chr2 + 230245862 230245940 230247915 230248065
KIAA1841 chr2 + 61073457 61073551 61076919 61077158
TNNT3 chr11 + 1926469 1926481 1929809 1929828
ARFIP1 chr4 + 152807203 152807248 152809672 152809733
TUBD1 chr17 − 59866608 59866749 59874538 59874703
POMZP3 chr7 − 76611453 76611591 76618182 76618300
SH3TC1 chr4 + 8225174 8225216 8226979 8228644
POLR2J4 chr7 − 43986600 43986677 44013592 44013679
CDKL3 chr5 − 134308573 134308727 134312291 134312380
CD300LF chr17 − 74696194 74696217 74698368 74698481
ELP1 chr9 − 108918810 108918901 108919252 108919349
RPTOR chr17 + 80707840 80707999 80730559 80730706
ZNF266 chr19 − 9434074 9434235 9434797 9434859
POLR2J4 chr7 − 43986600 43986677 43987677 43987888
CBWD3 chr9 + 68266219 68266306 68268933 68268978
WDR12 chr2 − 202894580 202894626 202897299 202897415
PVT1 chr8 + 128009589 128009718 128082752 128082848
LLGL2 chr17 + 75574212 75574260 75574609 75574668
TCFL5 chr20 − 62854015 62854157 62859363 62859526
MCTP1 chr5 − 94870416 94870491 94870871 94870973
ST3GAL5 chr2 − 85852859 85853099 85861180 85861292
UBXN8 chr8 + 30754664 30754787 30756764 30756887
ATXN2 chr12 − 111464661 111464715 111470107 111470240
MICA chr6 + 31410542 31410797 31411946 31412225
CARD8 chr19 − 48242539 48242644 48246074 48246381
CARD8 chr19 − 48242539 48242644 48246074 48246381
AL121845.3 chr20 + 63735158 63735564 63737532 63737647
IL32 chr16 + 3067983 3068010 3068179 3068239
GMPPB chr3 − 49722431 49722510 49722595 49722754
ZEB2 chr2 − 144403915 144404130 144424795 144424867
TBC1D8 chr2 − 101032267 101032385 101033543 101033758
LEMD3 chr12 + 65245668 65245774 65245860 65245939
SLC38A1 chr12 − 46201097 46201198 46203009 46203089
JARID2 chr6 + 15468541 15468718 15487306 15487542
SLC38A9 chr5 − 55633694 55635657 55645788 55645895
AC119396.1 chr19 + 7362780 7362905 7372811 7373071
UBE3C chr7 + 157216866 157216971 157220688 157220776
MARCHF8 chr10 − 45461230 45461411 45489366 45489417
TUBGCP4 chr15 + 43400043 43400221 43401715 43401850
SLAMF1 chr1 − 160624095 160624185 160634612 160634897
GTF2H2 chr5 − 71045443 71045507 71048005 71048113
IRF8 chr16 + 85913130 85913236 85918416 85918803
POMZP3 chr7 − 76611453 76611591 76611721 76611813
MCM6 chr2 − 135862606 135862748 135866131 135866277
PVT1 chr8 + 128070161 128070272 128082752 128082848
NIBAN3 chr19 + 17537375 17537543 17539149 17539265
NFS1 chr20 − 35675044 35675202 35680736 35680871
KDM3B chr5 + 138381515 138381590 138391012 138392261
AC114490.2 chr1 − 34983766 34983947 34992233 34992387
ZC3H13 chr13 − 46020448 46020557 46042163 46042275
TGS1 chr8 + 55786237 55787060 55790181 55790299
CR1 chr1 + 207609289 207609688 207611676 207611853
POMZP3 chr7 − 76618182 76618300 76625521 76625683
POMZP3 chr7 − 76618182 76618615 76625521 76625683
DDX21 chr10 + 68971890 68972052 68973544 68973664
SYNE1 chr6 − 152176393 152176560 152180135 152180294
ZBTB17 chr1 − 15945714 15945840 15946934 15947123
MYOM1 chr18 − 3075724 3075761 3079178 3079342
TIMM23B-AGAP6 chr10 + 49987164 49987234 49988750 49988938
SBNO1 chr12 − 123315547 123315660 123317220 123317356
RAB11FIP3 chr16 + 491133 491268 496823 496859
CNOT1 chr16 − 58558472 58558674 58560211 58560362
NMRK1 chr9 − 75069741 75069813 75069894 75070042
IRF8 chr16 + 85914472 85914520 85918416 85918803
TSC2 chr16 + 2079275 2079428 2079556 2079669
RCHY1 chr4 − 75491888 75491933 75494100 75494179
PVT1 chr8 + 128070159 128070361 128082752 128082848
COG8 chr16 − 69330812 69331095 69332713 69332882
FKBP15 chr9 − 113206508 113206578 113207211 113207296
PLBD1-AS1 chr12 + 14614521 14614570 14619151 14619373
TOM1 chr22 + 35345724 35345784 35346929 35346969
SUGP1 chr19 − 19296988 19297344 19310096 19310200
MCTP1 chr5 − 94708511 94708609 94710817 94710927
ZNF185 chrX + 152920706 152920748 152922172 152922256
TAF1D chr11 − 93733086 93733121 93733349 93733397
CELF1 chr11 − 47476845 47476959 47477296 47477425
PIGG chr4 + 515972 516185 523458 523913
C11orf80 chr11 + 66762078 66762450 66788159 66788269
ZNF638 chr2 + 71408121 71408247 71418601 71418639
TRIM14 chr9 − 98091908 98092001 98094866 98095029
NEIL2 chr8 + 11771445 11771585 11783202 11783399
SNX9 chr6 + 157896826 157896998 157901897 157902045
NSUN6 chr10 − 18585948 18586093 18596207 18596327
MRTFA chr22 − 40420846 40421100 40423535 40423685
SLC3A2 chr11 + 62884631 62884690 62885176 62885608
SNAPC1 chr14 + 61782246 61782397 61792806 61792902
ING4 chr12 − 6652944 6653050 6656726 6656798
SERF2 chr15 + 43801131 43801187 43801517 43801569
FAM114A2 chr5 − 154034277 154034377 154034743 154034967
CELF1 chr11 − 47476845 47476956 47477296 47477425
NFKB2 chr10 + 102398211 102398297 102398738 102398864
VARS1 chr6 − 31782529 31782633 31782720 31782845
CLEC17A chr19 + 14599716 14599812 14600030 14600182
TMEM184B chr22 − 38225423 38225593 38226778 38226870
EML2 chr19 − 45619059 45619191 45626704 45626839
CCM2 chr7 + 45038252 45038426 45064462 45064646
WRNIP1 chr6 + 2770119 2770361 2779262 2779492
DENND4B chr1 − 153932641 153932777 153932860 153933030
AL392172.1 chr1 + 222835118 222835215 222836995 222837066
TMEM131 chr2 − 97796843 97796986 97797364 97797516
RYK chr3 − 134191848 134191974 134195081 134195182
TMCO3 chr13 + 113534044 113534240 113547299 113547379
FOXP1 chr3 − 70965889 70966056 70970735 70970805
DNMT1 chr19 − 10139675 10139817 10140780 10140909
ZNF254 chr19 + 24105939 24106066 24106547 24106643
TCFL5 chr20 − 62854015 62854157 62859363 62859526
PILRB chr7 + 100355142 100355240 100356749 100356883
IDH1 chr2 − 208239070 208239233 208241993 208242145
NUP98 chr11 − 3699081 3699348 3702462 3702892
DDB2 chr11 + 47234756 47234934 47235269 47235412
IGHD chr14 − 105840900 105841224 105841960 105842032
POLR2J3 chr7 − 102543524 102543702 102566581 102566736
UBAP2L chr1 + 154266500 154266568 154268756 154268954
TSEN2 chr3 + 12505153 12505231 12516610 12516661
COA1 chr7 − 43650611 43650712 43656032 43656153
MPHOSPH6 chr16 − 82149308 82149403 82151423 82151514
CERS4 chr19 + 8257878 8257985 8261687 8261844
AC069281.2 chr7 − 100577272 100577389 100577496 100577558
ATP2B4 chr1 + 203722477 203722689 203723880 203723988
EIF4G1 chr3 + 184324877 184325114 184325268 184325373
WDFY3 chr4 − 84678918 84679242 84682373 84682470
ECPAS chr9 − 111378579 111378730 111383210 111383332
SLC25A19 chr17 − 75278151 75278335 75283422 75283593
STAU2 chr8 − 73697307 73697442 73709031 73709177
RPS6KA3 chrX − 20195064 20195145 20204021 20204103
DUS2 chr16 + 68075354 68075504 68076631 68076719
MAN1B1 chr9 + 137101483 137101672 137106124 137106315
KMT2D chr12 − 49022589 49022875 49024577 49024708
RRP8 chr11 − 6600668 6600775 6600925 6601602
SPAG9 chr17 − 50977107 50977221 50979745 50979917
CPNE1 chr20 − 35627279 35627413 35630740 35630795
UBXN11 chr1 − 26297426 26297481 26297961 26298062
SLC44A2 chr19 + 10635430 10635515 10636322 10636585
KDM5A chr12 − 356431 356537 362962 363097
TNPO1 chr5 + 72897055 72897151 72900005 72900081
HEATR5B chr2 − 36988645 36988859 36990647 36990799
RNF170 chr8 − 42865415 42865489 42870003 42870112
RHOT1 chr17 + 32176160 32176213 32183170 32183272
TMEM50B chr21 − 33439213 33439297 33448781 33448879
SCLT1 chr4 − 128888678 128888774 128891058 128891137
MAN2B1 chr19 − 12648174 12648402 12649135 12649216
PCBP1-AS1 chr2 − 69988741 69988838 69996685 69996888
AC069281.2 chr7 − 100577496 100577558 100577663 100577740
DTNBP1 chr6 − 15637743 15637804 15651312 15651363
PINK1 chr1 + 20644489 20644672 20645559 20645723
HDAC7 chr12 − 47795905 47796016 47796214 47796298
CMTM1 chr16 + 66571136 66571270 66577103 66577202
CDC23 chr5 − 138191861 138191937 138192268 138192388
PCBP1-AS1 chr2 − 70055713 70055910 70083506 70083687
PCBP1-AS1 chr2 − 70055713 70055910 70083537 70083687
EHBP1L1 chr11 + 65579935 65579989 65580080 65580259
ANKZF1 chr2 + 219234132 219234288 219234825 219235312
AC118553.2 chr1 + 100049908 100050004 100058665 100058728
NAE1 chr16 − 66816580 66816672 66816964 66817028
GIT1 chr17 − 29575629 29575703 29575811 29575898
CREBBP chr16 − 3770569 3770986 3773750 3773930
RALY chr20 + 34073818 34073866 34075873 34076040
XAF1 chr17 + 6759255 6759718 6760405 6760601
CCM2 chr7 + 45038252 45038426 45063917 45064001
CPSF7 chr11 − 61416104 61416162 61416363 61416519
CAST chr5 + 96740037 96740118 96740744 96740783
SMG5 chr1 − 156259004 156259163 156260450 156260626
PVT1 chr8 + 128070159 128070272 128082752 128082848
RGS6 chr14 + 72518350 72518537 72536185 72536275
SUMF2 chr7 + 56074173 56074218 56074585 56074736
RALY chr20 + 34073818 34073866 34075873 34076040
RALY chr20 + 34073818 34073866 34075873 34076040
MLKL chr16 − 74678898 74678980 74682650 74682786
ITPA chr20 + 3218516 3218632 3221840 3221917
GATAD2A chr19 + 19494293 19494383 19495753 19495885
MKNK1 chr1 − 46568442 46568498 46572062 46572167
MIR4435-2HG chr2 − 111248147 111248241 111344060 111344237
SSBP4 chr19 + 18427897 18427982 18430840 18430930
CCM2 chr7 + 45038252 45038426 45063917 45064001
TNFRSF1A chr12 − 6329777 6330066 6330852 6330926
TLE3 chr15 − 70056297 70056374 70057458 70057658
ARHGAP25 chr2 + 68775220 68775420 68782232 68782320
TRAK1 chr3 + 42200817 42201054 42202435 42202752
LRCH3 chr3 + 197858833 197858905 197865422 197865471
TLE3 chr15 − 70056297 70056374 70057473 70057658
PLD3 chr19 + 40366772 40366915 40367695 40367879
ADA chr20 − 44623006 44623078 44624201 44624329
SHISA5 chr3 − 48469360 48469573 48469727 48469843
NCF1 chr7 + 74787983 74788088 74788558 74788704
NUP88 chr17 − 5387778 5387904 5388801 5388960
USB1 chr16 + 58014272 58014326 58017333 58017439
FMNL1 chr17 + 45240475 45240625 45241128 45241230
CYB5R4 chr6 + 83914415 83914448 83922437 83922470
NFKB2 chr10 + 102398384 102398523 102399287 102399497
NUP88 chr17 − 5387778 5387952 5388801 5388960
RCBTB2 chr13 − 48511769 48511877 48512015 48512174
STRADA chr17 − 63713405 63713527 63714005 63714108
CRTC2 chr1 − 153951259 153951666 153952017 153952262
UNC13D chr17 − 75839838 75839942 75840017 75840110
ICE1 chr5 + 5460435 5465226 5466333 5466502
TMBIM1 chr2 − 218278514 218278565 218279037 218279091
SH2D3C chr9 − 127747146 127747271 127749210 127749665
SLC44A2 chr19 + 10635162 10635255 10635430 10635515
SORL1 chr11 + 121488031 121488193 121490042 121490110
LTBR chr12 + 6386346 6386444 6388397 6388505
CHP1 chr15 + 41262755 41262883 41270556 41270618
CTDNEP1 chr17 − 7244550 7244635 7246025 7246137
RPS12 chr6 + 132816460 132816563 132816959 132817061
WDFY4 chr10 + 48963841 48964054 48966525 48966673
FANCA chr16 − 89748658 89748767 89749729 89749902
CPNE1 chr20 − 35627279 35627413 35630438 35631034
CPNE1 chr20 − 35627279 35627413 35630900 35631034
OSBPL11 chr3 − 125563697 125563843 125567393 125567595
RHOT1 chr17 + 32176160 32176213 32182756 32182865
ITGAL chr16 + 30513770 30513846 30516972 30517086
INTS8 chr8 + 94831991 94832174 94836523 94836631
DBNL chr7 + 44058431 44058480 44058901 44058983
GSN chr9 + 121321267 121321401 121324553 121324644
CNOT3 chr19 + 54146600 54146657 54148147 54148535
DAGLB chr7 − 6421726 6421804 6425987 6426114
DBNL chr7 + 44058431 44058480 44058877 44058983
STXBP2 chr19 + 7645196 7645306 7646248 7646344
SNHG29 chr17 + 16439527 16439703 16440184 16440253
UNC13D chr17 − 75831097 75831169 75831242 75831348
FCHO1 chr19 + 17766668 17766810 17770424 17770577
SLC35C2 chr20 − 46350760 46350890 46352050 46352226
WDR47 chr1 − 108981732 108981864 108982608 108982785
MKNK2 chr19 − 2041039 2041204 2041839 2042034
INPP5D chr2 + 233125747 233125919 233130507 233130648
LRCH4 chr7 − 100576901 100577005 100577496 100577558
TTC7A chr2 + 47011330 47011435 47021861 47021979
UNC93B1 chr11 − 67997674 67997799 67998358 67998452
PDE4B chr1 + 66363406 66363571 66365666 66365766
HLA-DRB1 chr6 − 32581556 32581838 32584108 32584378
TNFRSF1A chr12 − 6329777 6330066 6330266 6330295
AC118553.2 chr1 + 100017681 100017815 100049908 100050004
FGR chr1 − 27615688 27615844 27616856 27617006
COG4 chr16 − 70481358 70481487 70481763 70481865
FLOT1 chr6 − 30740678 30740798 30741613 30741704
CAMK1D chr10 + 12791157 12791233 12814194 12814307
LMBR1 chr7 − 156724111 156724178 156734176 156734257
TSC2 chr16 + 2058746 2058873 2060669 2060813
FGR chr1 − 27621558 27621657 27625088 27625151
NAA60 chr16 + 3448470 3448540 3479470 3479600
INTS6 chr13 − 51395299 51395483 51423029 51423090
TTC16 chr9 + 127724755 127724897 127726238 127726404
H2AZ2 chr7 − 44835528 44835658 44843276 44843354
AC004997.1 chr22 − 30288705 30288776 30292772 30292851
SPTLC1 chr9 − 92076797 92077035 92079433 92079566
BAG6 chr6 − 31640384 31640528 31640644 31640704
TTC17 chr11 + 43414589 43414776 43436163 43436334
CDK16 chrX + 47227378 47227469 47228566 47228644
NAXD chr13 + 110622215 110622366 110624233 110624279
IGFLR1 chr19 − 35739709 35740086 35740379 35740564
GOLGA7 chr8 + 41490832 41490965 41497508 41497661
YY1AP1 chr1 − 155679408 155679512 155680415 155680456
YY1AP1 chr1 − 155679408 155679512 155680415 155680456
CASC4 chr15 + 44328684 44328787 44338236 44338317
PTDSS1 chr8 + 96284108 96284153 96287021 96287146
CEP290 chr12 − 88059897 88060020 88060829 88060994
TIMM23B-AGAP6 chr10 + 49973011 49973142 49987164 49987234
IL21R chr16 + 27430055 27430120 27434346 27434449
DNMT1 chr19 − 10180777 10180885 10182040 10182077
PDIA4 chr7 − 149005140 149005374 149005896 149006053
SIPA1 chr11 + 65647383 65647658 65649261 65649480
POLR2F chr22 + 37956772 37956842 37959345 37959476
POLL chr10 − 101582762 101582891 101583507 101583681
PSMA5 chr1 − 109415236 109415363 109421859 109421926
PAFAH2 chr1 − 25989447 25989601 25990726 25990921
MOV10 chr1 + 112674847 112675049 112688934 112689138
HMGB2 chr4 − 173333068 173333214 173333499 173333669
PYCR2 chr1 − 225922203 225922383 225923700 225923771
B4GALT3 chr1 − 161173858 161174049 161176433 161176579
RHOT2 chr16 + 672488 672566 672702 672825
DDX17 chr22 − 38494629 38494802 38495795 38495937
NQO2 chr6 + 3004494 3004651 3006467 3006559
WDR70 chr5 + 37437921 37437981 37443238 37443372
INTS8 chr8 + 94841490 94841591 94842346 94842488
EXOSC1 chr10 − 97441170 97441259 97445731 97445847
RABEPK chr9 + 125203007 125203066 125213369 125213522
UTP6 chr17 − 31884423 31884505 31885979 31886061
TRPC4AP chr20 − 35021189 35021356 35035122 35035308
XAF1 chr17 + 6759661 6759718 6762154 6762240
ZDHHC4 chr7 + 6578565 6578720 6580554 6580678
PHYKPL chr5 − 178224447 178224564 178231404 178231523
CAST chr5 + 96675538 96675601 96695835 96695907
PPA2 chr4 − 105437949 105438036 105453597 105453642
RBM6 chr3 + 49972058 49972148 49975322 49975392
DDX21 chr10 + 68974669 68974743 68977528 68977688
RCBTB2 chr13 − 48502723 48502914 48510628 48510771
ABCA7 chr19 + 1050920 1051052 1051154 1051294
LMF2 chr22 − 50506284 50506502 50506637 50506666
PHC2 chr1 − 33332274 33332404 33334184 33334292
WDSUB1 chr2 − 159248371 159248512 159259809 159259843
JAK1 chr1 − 64883276 64883475 64886258 64886341
IFTAP chr11 + 36610080 36610239 36633283 36633438
RABEPK chr9 + 125207563 125207721 125213369 125213522
SNX10 chr7 + 26346419 26346466 26360974 26361061
DAGLB chr7 − 6432836 6432959 6445952 6446104
DEK chr6 − 18257952 18258062 18258303 18258405
WDSUB1 chr2 − 159248371 159248512 159271701 159271795
LAIR1 chr19 − 54360915 54361209 54364294 54364330
VDAC2 chr10 + 75212229 75212298 75214020 75214070
PPP4R3B chr2 − 55598415 55599039 55603977 55604076
DLEU2 chr13 − 50044639 50044768 50049583 50049662
STK38 chr6 − 36525590 36525642 36540071 36540207
STAT5B chr17 − 42227528 42227685 42231999 42232137
DESI1 chr22 − 41604043 41604153 41607261 41607331
CCM2 chr7 + 45038252 45038426 45069825 45069961
PREX1 chr20 − 48708259 48708421 48747808 48747880
TMEM87A chr15 − 42233212 42233306 42236319 42236419
NEPRO chr3 − 113011044 113011406 113012733 113013403
WDR37 chr10 + 1072115 1072293 1077906 1078003
LAIR1 chr19 − 54360915 54361206 54364294 54364330
LAIR1 chr19 − 54360915 54361243 54364294 54364330
SUPT20H chr13 − 37047534 37047601 37047877 37047936
CDC16 chr13 + 114236644 114236699 114236798 114236896
JPX chrX + 73946998 73947374 73994863 73994961
RBM23 chr14 − 22911785 22911903 22913723 22913845
RPL18A chr19 + 17861292 17861472 17862093 17862223
LINC00893 chrX − 149529512 149529593 149532881 149533055
ZDHHC4 chr7 + 6578565 6578746 6580554 6580678
SND1 chr7 + 127686612 127686762 127694827 127694948
SLC3A2 chr11 + 62881892 62882066 62882907 62882999
RBM33 chr7 + 155700772 155700944 155706859 155707068
TMEM63A chr1 − 225867887 225868030 225871075 225871113
MEF2D chr1 − 156477011 156477202 156479289 156479346
NLRC5 chr16 + 57028071 57028385 57029772 57029856
POLD2 chr7 − 44117942 44118064 44121833 44122109
TNFSF13 chr17 + 7559623 7559702 7560048 7560167
NTAN1 chr16 − 15044333 15044407 15047417 15047550
VPS53 chr17 − 661808 661895 697417 697484
TANGO2 chr22 + 20036759 20037094 20043354 20043443
ARHGEF40 chr14 + 21073044 21073242 21073931 21075180
ZDHHC24 chr11 − 66526935 66527006 66543703 66543981
ABCA7 chr19 + 1055906 1055939 1056065 1056243
SAMD9L chr7 − 93144731 93144833 93145384 93145532
EPSTI1 chr13 − 42953947 42954021 42969093 42970670
POLR3C chr1 + 145833489 145833582 145838055 145838206
ECHDC1 chr6 − 127316449 127316502 127330808 127331030
GMDS-DT chr6 + 2269697 2269799 2271815 2273417
WDSUB1 chr2 − 159256195 159256375 159271701 159271795
TYROBP chr19 − 35907445 35907580 35907729 35907762
TTC13 chr1 − 230931297 230931472 230931735 230931877
PHF20L1 chr8 + 132814636 132814889 132816887 132817076
CORO1C chr12 − 108662028 108662158 108701123 108701323
ECHDC1 chr6 − 127316449 127316502 127326997 127327144
SMIM8 chr6 + 87337008 87337166 87371592 87371712
NEPRO chr3 − 113011044 113011165 113012733 113013403
HLA-C chr6 − 31269337 31269385 31269492 31269525
BBS9 chr7 + 33357854 33357995 33367766 33367862
AMD1 chr6 + 110887504 110887591 110888856 110888983
ERCC1 chr19 − 45413962 45414034 45414860 45414960
DLG1 chr3 − 197194424 197194589 197282678 197282845
ZFAND1 chr8 − 81713917 81714039 81714803 81715114
MAPKAPK5 chr12 + 111865249 111865323 111867571 111867669
CELF1 chr11 − 47473087 47473231 47475335 47475521
PVT1 chr8 + 127795893 127796008 128070159 128070272
WASH3P chr15 + 101966069 101966223 101971822 101972049
CNOT2 chr12 + 70278131 70278274 70310894 70311017
RFFL chr17 − 35021370 35021781 35026373 35026561
LONP2 chr16 + 48258617 48258740 48261423 48261587
ARIH2 chr3 + 48961611 48961679 48967124 48967275
SNX22 chr15 + 64152637 64152742 64153651 64153684
SCAP chr3 − 47417121 47417207 47417303 47417823
VASP chr19 + 45522717 45522818 45523840 45523877
FKBP15 chr9 − 113199813 113199963 113202530 113202629
PSD4 chr2 + 113184956 113185073 113185364 113185440
INTS8 chr8 + 94838462 94838618 94842346 94842488
TANGO2 chr22 + 20036759 20036854 20043354 20043443
TMEM127 chr2 − 96254832 96254997 96265137 96265512
LRCH3 chr3 + 197854391 197854445 197858833 197858905
KDM5C chrX − 53218275 53218398 53220838 53220916
BBS1 chr11 + 66519616 66519748 66521269 66521376
SRP14-AS1 chr15 + 40056452 40056641 40064295 40064601
SOS1 chr2 − 38987472 38987591 38995122 38995387
RNF121 chr11 + 71994718 71994852 71995439 71995551
PDCD6 chr5 + 272710 272772 311292 311402
SEC16A chr9 − 136451255 136451408 136453427 136453510
ADAP2 chr17 + 30931888 30931968 30934184 30934297
DNAJC2 chr7 − 103337735 103337811 103341763 103341865
RPS6KB1 chr17 + 59914634 59914703 59926434 59926582
RNF121 chr11 + 71994718 71994852 71995449 71995551
CEP290 chr12 − 88059897 88060020 88060829 88060994
PVT1 chr8 + 127795893 127796071 128070159 128070272
EXOSC9 chr4 + 121802914 121803017 121804621 121804759
CLPTM1 chr19 + 44961962 44962075 44973086 44973210
PREX1 chr20 − 48734545 48734650 48747808 48747880
IL15 chr4 + 141688821 141689035 141720468 141720566
MTA1 chr14 + 105445417 105445511 105450057 105450184
EFCAB13 chr17 + 47361377 47361521 47391436 47391580
OCEL1 chr19 + 17226993 17227199 17228255 17228309
ZC3H7A chr16 − 11763477 11763659 11765052 11765153
DAGLB chr7 − 6416258 6416754 6416840 6416921
EIF2B4 chr2 − 27368371 27368463 27369005 27369212
EIF2D chr1 − 206599002 206599092 206599462 206599612
GUSBP11 chr22 − 23705428 23705541 23709129 23709241
FBXO3 chr11 − 33768850 33769014 33770740 33770830
VASP chr19 + 45522717 45522818 45523643 45523695
GRK3 chr22 + 25703509 25703576 25704108 25704209
PIK3AP1 chr10 − 96656797 96656934 96709566 96709983
CDC16 chr13 + 114236644 114236699 114236801 114236896
RALGAPB chr20 + 38565358 38565478 38570768 38570847
PAPSS1 chr4 − 107693770 107694006 107701170 107701285
RABGAP1L chr1 + 174370978 174371072 174393994 174394145
C1orf21 chr1 + 184477385 184477603 184507587 184507682
LAIR1 chr19 − 54360021 54360072 54361009 54361209
ST6GAL1 chr3 + 187038741 187038873 187042653 187043310
OGFOD1 chr16 + 56466151 56466268 56466875 56466967
ARAP2 chr4 − 36046709 36046849 36052005 36052053
FDX1 chr11 + 110435833 110435958 110456917 110457047
TTC39B chr9 − 15225916 15226012 15267913 15267948
CD320 chr19 − 8302776 8302980 8303854 8304088
RUNX3 chr1 − 24919239 24919344 24927573 24927730
COP1 chr1 − 176163814 176163891 176175909 176176007
ANKRD27 chr19 − 32644324 32644479 32646458 32646615
TXLNA chr1 + 32180313 32180514 32184524 32184616
TPGS2 chr18 − 36807846 36807934 36818893 36818973
MCTP1 chr5 − 94942347 94942427 94953218 94953361
AD000671.1 chr19 + 35752803 35752833 35752913 35752999
COQ7 chr16 + 19075720 19075860 19077305 19077374
NRF1 chr7 + 129657342 129657574 129671428 129671543
IFTAP chr11 + 36610080 36610239 36633283 36633438
SCFD1 chr14 + 30633946 30634037 30638124 30638247
LY96 chr8 + 74010000 74010129 74026788 74026841
TMCO4 chr1 − 19770541 19770569 19780579 19780766
ANKZF1 chr2 + 219231927 219232040 219232259 219232362
SCYL1 chr11 + 65537966 65538182 65538269 65538324
PTPRA chr20 + 2923206 2923285 2986764 2986849
DRAM1 chr12 + 101897862 101897930 101908185 101908363
USP48 chr1 − 21747066 21747149 21748137 21748271
ARHGEF40 chr14 + 21076562 21076643 21076773 21076890
CHFR chr12 − 132877554 132877654 132887195 132887340
GYS1 chr19 − 48978097 48978157 48981529 48981636
RORC chr1 − 151813238 151813346 151813487 151813702
UVRAG chr11 + 76004004 76004089 76007533 76007621
SIRPB1 chr20 − 1566152 1566267 1578337 1578694
TTI2 chr8 − 33509745 33509932 33511966 33512712
COP1 chr1 − 176149005 176149074 176184632 176184692
TMEM8B chr9 + 35829876 35829955 35834460 35834650
CAPN12 chr19 − 38734318 38734389 38735369 38735429
HIPK3 chr11 + 33286412 33287511 33328509 33328633
SRC chr20 + 37401601 37401678 37402434 37402588
HERPUD2 chr7 − 35667433 35667588 35694183 35694627
KLRG1 chr12 + 8992205 8992310 9008974 9009075
COP1 chr1 − 176149005 176149074 176175909 176176007
WDSUB1 chr2 − 159257757 159257864 159271701 159271795
SPG7 chr16 + 89526328 89526468 89529476 89529579
P4HA1 chr10 − 73043886 73043957 73044980 73045051
IKBKG chrX + 154558531 154558650 154560406 154560559
METTL26 chr16 − 634888 634956 635280 635340
DNAJC1 chr10 − 21920797 21920963 21929039 21929141
NACC2 chr9 − 136016264 136016429 136049635 136050580
THOC6 chr16 + 3025923 3025988 3026062 3026166
ALG13 chrX + 111682131 111682235 111682235 111682294
RB1 chr13 + 48376917 48377034 48380052 48380084
LRP8 chr1 − 53266472 53266647 53275630 53275753
BCAS3 chr17 + 60947218 60947352 60989970 60990235
RNF170 chr8 − 42870003 42870112 42873930 42874006
MDM4 chr1 + 204530683 204530817 204532190 204532246
METTL26 chr16 − 634888 635063 635280 635340
FANCA chr16 − 89758576 89758705 89761948 89762022
CWF19L1 chr10 − 100260217 100260319 100261978 100262063
LRRK2 chr12 + 40251464 40251544 40252909 40253016
PRMT9 chr4 − 147642786 147642940 147653851 147654566
NUP54 chr4 − 76134174 76134362 76136185 76136412
ANKZF1 chr2 + 219230227 219230405 219232259 219232362
NAE1 chr16 − 66821449 66821559 66823226 66823306
PPP2R2D chr10 + 131901237 131901330 131934457 131934555
TSEN2 chr3 + 12516610 12516661 12519058 12519197
IKBKG chrX + 154558531 154558650 154560406 154560559
THEM4 chr1 − 151889213 151889373 151895007 151895194
COP1 chr1 − 176149005 176149074 176175909 176176007
CAST chr5 + 96740744 96740783 96741265 96741358
AGPAT3 chr21 + 43903956 43904019 43959633 43959859
TRPM7 chr15 − 50586391 50586488 50589591 50589656
RAD1 chr5 − 34911553 34911812 34914694 34914961
RNPC3 chr1 + 103527694 103527742 103533738 103533857
WDSUB1 chr2 − 159257757 159257864 159259809 159259843
SLBP chr4 − 1700010 1700070 1703595 1703700
KIF1C chr17 + 4999849 4999970 5000219 5000352
FOXRED1 chr11 + 126274926 126275021 126275326 126275428
DICER1-AS1 chr14 + 95158192 95158234 95158875 95159035
CRBN chr3 − 3154746 3154831 3156218 3156281
PACC1 chr1 − 212375192 212375300 212379894 212380037
SPATA13 chr13 + 24284134 24284271 24286213 24286393
ABCB7 chrX − 75076521 75076654 75098941 75099061
DENND4B chr1 − 153933196 153933319 153933482 153933871
JAK2 chr9 + 4985939 4986022 5021962 5022213
N4BP2L1 chr13 − 32404320 32404397 32407249 32407338
IMMP1L chr11 − 31460625 31460714 31473723 31473786
TBC1D2B chr15 − 78044899 78045068 78054033 78054187
ATF7IP chr12 + 14423908 14425473 14434339 14434423
SLBP chr4 − 1700010 1700091 1703595 1703700
ARHGAP19 chr10 − 97256317 97256404 97259401 97259628
POLL chr10 − 101582762 101582891 101587245 101587406
IL15 chr4 + 141656185 141656307 141719365 141719476
RIN3 chr14 + 92555750 92555955 92615406 92615479
PXN chr12 − 120216272 120216581 120219206 120220091
PLXDC1 chr17 − 39109247 39109391 39139653 39139832
N4BP2L1 chr13 − 32404320 32404397 32407644 32407772
PI4KAP2 chr22 − 21487871 21488023 21491993 21492094
SUZ12P1 chr17 + 30734896 30734943 30735032 30735097
SCAF8 chr6 + 154778000 154778045 154787860 154788022
GTF2IRD2B chr7 + 75112396 75112535 75120890 75121010
SENP6 chr6 + 75623899 75623960 75634706 75634811
DNMT3A chr2 − 25246619 25246776 25247590 25247749
DCP1B chr12 − 1993263 1993391 1997934 1997975
TMEM39A chr3 − 119452446 119452530 119458017 119458240
CBWD3 chr9 + 68269599 68269722 68270301 68270518
RETSAT chr2 − 85345974 85346094 85350779 85351021
DENND6A chr3 − 57633264 57633354 57634557 57634622
ZSWIM7 chr17 − 15977578 15977700 15977799 15977913
AK5 chr1 + 77286940 77287127 77293792 77293960
MDM1 chr12 − 68326656 68327021 68331106 68331221
ITGA6 chr2 + 172467480 172467560 172470973 172471105
HDAC4 chr2 − 239163802 239163923 239176412 239176563
SIRPB1 chr20 − 1571719 1572037 1578337 1578694
ELMO2 chr20 − 46380252 46380303 46383415 46383494
ABCA7 chr19 + 1055096 1055351 1055906 1055939
HLA-B chr6 − 31355106 31355223 31356687 31356957
KIAA0753 chr17 − 6622881 6623097 6623508 6623571
MRNIP chr5 − 179847977 179848066 179853196 179853276
RIOK1 chr6 + 7395052 7395143 7396702 7396772
HLA-B chr6 − 31355316 31355592 31356687 31356957
RNF144B chr6 + 18399498 18399699 18427580 18427685
RAB35 chr12 − 120099029 120099154 120108416 120108467
DOCK10 chr2 − 224916694 224916784 224931548 224931668
FBXL4 chr6 − 98917373 98917719 98934761 98934879
TMEM189-UBE2V1 chr20 − 50130855 50130947 50143501 50143621
SEPTIN11 chr4 + 76996424 76996539 77005600 77005796
RBM22 chr5 − 150699241 150699271 150700443 150700497
BSCL2 chr11 − 62702467 62702549 62705467 62705617
SNHG17 chr20 − 38422091 38422241 38426418 38426503
SORBS3 chr8 + 22566344 22566484 22566660 22566868
SPOPL chr2 + 138550156 138550294 138550482 138550604
SLC7A6 chr16 + 68274690 68275249 68287745 68287871
NDRG1 chr8 − 133280231 133280267 133284248 133284329
LAIR1 chr19 − 54361009 54361209 54364294 54364330
LAIR1 chr19 − 54361009 54361243 54364294 54364330
ATL2 chr2 − 38309378 38309506 38343267 38343512
SCAF8 chr6 + 154773988 154774072 154787860 154788022
AC009061.2 chr16 + 67484109 67484328 67492024 67492121
TMCO4 chr1 − 19770541 19770569 19771307 19771482
BSCL2 chr11 − 62702467 62702549 62705300 62705617
MAPK6 chr15 + 52045829 52047015 52049992 52050137
PLSCR3 chr17 − 7393466 7393509 7394103 7394267
FOXJ3 chr1 − 42188736 42188928 42189302 42189404
SLC39A11 chr17 − 72947730 72947875 73031555 73031714
PYROXD1 chr12 + 21440367 21440448 21445346 21445466
RNF144B chr6 + 18399498 18399699 18459606 18459751
TMEM220 chr17 − 10725010 10725134 10726203 10726264
TADA2A chr17 + 37442563 37442652 37444695 37444768
CYRIB chr8 − 129912469 129912515 129948965 129949067
PEX1 chr7 − 92518994 92519078 92522101 92522245
TSPAN2 chr1 − 115058882 115058981 115072904 115073007
TTLL12 chr22 − 43180741 43180940 43182979 43183149
TMEM234 chr1 − 32216383 32216517 32216888 32216947
BCL9L chr11 − 118909913 118910015 118918825 118918879
AC008073.3 chr2 + 24164197 24164335 24177801 24177870
GNB4 chr3 − 179419398 179419505 179420888 179420927
TSPAN2 chr1 − 115060463 115060538 115072904 115073007
TMEM234 chr1 − 32215135 32215216 32216888 32216947
ERAP2 chr5 + 96896731 96896863 96900120 96900245
ANKRD6 chr6 + 89606006 89606105 89612271 89612370
DDX60L chr4 − 168394460 168394617 168395958 168396127
GTF2H2B chr5 + 70434178 70434266 70434914 70435022
SLC35F2 chr11 − 107804717 107804770 107805358 107805515
TBCD chr17 + 82763964 82764062 82766266 82766368
ZFR chr5 − 32417647 32417792 32419820 32420103
PXYLP1 chr3 + 141260122 141260254 141278341 141278500
SOS1 chr2 − 39058672 39058804 39067627 39067753
SNHG17 chr20 − 38422086 38422241 38425934 38426052
CA5B chrX + 15721496 15721592 15745630 15745710
SNHG17 chr20 − 38422091 38422241 38425934 38426052
ERC1 chr12 + 1263033 1263165 1289851 1290012
CYRIB chr8 − 129912469 129912515 129948965 129949067
RANBP10 chr16 − 67772033 67772086 67805427 67805539
AC092070.2 chr19 + 53200623 53200703 53204015 53204142
SETD6 chr16 + 58516477 58516672 58516807 58516928
ITGB2 chr21 − 44910283 44910372 44910724 44910785
CEP170 chr1 − 243142366 243142463 243156220 243156347
SNHG17 chr20 − 38422086 38422241 38422290 38422368
LRP8 chr1 − 53262067 53262207 53264168 53264396
SNHG17 chr20 − 38422091 38422241 38422290 38422368
ANKRD36B chr2 − 97515731 97515945 97523325 97523467
GeneID IncFormLen SkipFormLen PValue FDR IncLevelDifference
CR1 298 298 5.48E−12 7.24E−09 0.438
PIGL 217 181 9.48E−08 2.53E−05 0.239
XPNPEP3 241 298 0.00048788 0.0195785 0.238
MAPKBP1 298 296 4.39E−05 0.0032844 0.231
TBC1D12 259 298 0.00020981 0.01073042 0.188
AC004593.2 261 188 0.00070623 0.02506553 0.184
AC016831.6 265 192 4.24E−06 0.00053836 0.184
WDR60 252 279 0.00102682 0.03186336 0.179
ZNF720 245 284 0.0002187 0.01104665 0.171
MYO15B 195 298 0.00016888 0.00909469 0.167
HSD17B3 225 257 0.0015585 0.04254252 0.165
WHAMMP3 298 279 0.00094552 0.03016446 0.164
AL392172.1 246 220 3.30E−05 0.00261998 0.163
ATXN2 203 298 0.00025889 0.01240124 0.152
AL356481.1 298 278 0.00055035 0.02126769 0.149
PDE8A 227 220 0.00048117 0.01943914 0.148
ZNF266 211 268 0.00177726 0.04646003 0.148
AL162258.1 217 265 3.47E−05 0.00273279 0.146
CAMKK1 283 186 0.00012409 0.00717412 0.145
PPFIA1 266 179 0.0014832 0.04131168 0.143
ZNF266 211 298 0.00055393 0.02130244 0.143
CFAP70 298 271 0.00026034 0.01245667 0.139
ACCS 209 220 0.00058237 0.02197879 0.138
ATF7IP2 216 235 7.24E−05 0.0047584 0.137
NEIL2 294 298 0.00065277 0.02401196 0.136
TAF4 239 298 4.42E−08 1.38E−05 0.129
PNPT1 207 252 0.00025212 0.01216099 0.128
HLA-DRB5 298 298 0.0009505 0.0302426 0.128
DDX60L 298 254 0.00155 0.04252019 0.126
YAF2 291 219 0.00039101 0.01661163 0.126
SP140 227 298 0.0011168 0.03387702 0.125
KIAA1841 243 298 0.00125417 0.03671553 0.125
TNNT3 161 168 1.22E−05 0.00123514 0.125
ARFIP1 194 210 0.00171986 0.04549068 0.12
TUBD1 298 290 0.0015442 0.04244113 0.12
POMZP3 267 287 0.00102346 0.03182082 0.117
SH3TC1 191 298 1.21E−05 0.00122804 0.117
POLR2J4 236 226 0.00010481 0.00636332 0.116
CDKL3 238 298 0.00089596 0.02913041 0.112
CD300LF 262 172 0.00169595 0.04510458 0.112
ELP1 246 240 0.00119097 0.0355404 0.111
RPTOR 298 296 9.05E−05 0.00569354 0.111
ZNF266 211 298 0.0011912 0.0355404 0.111
POLR2J4 298 226 0.000146 0.00815921 0.11
CBWD3 236 194 0.0001464 0.00817119 0.11
WDR12 265 195 8.91E−06 0.00098839 0.109
PVT1 278 245 5.56E−05 0.00395755 0.109
LLGL2 197 208 8.52E−05 0.00546071 0.107
TCFL5 298 291 0.00019662 0.01021553 0.104
MCTP1 251 224 9.96E−06 0.00108492 0.104
ST3GAL5 261 298 0.00151188 0.04186972 0.103
UBXN8 272 272 0.00048321 0.01948491 0.102
ATXN2 282 203 3.72E−06 0.0004904 0.102
MICA 298 298 5.91E−06 0.0007001 0.101
CARD8 298 254 0.00105347 0.03233151 0.101
CARD8 298 254 0.00171755 0.04545715 0.101
AL121845.3 298 264 3.17E−05 0.00255419 0.099
IL32 176 209 0.00097148 0.03059748 0.099
GMPPB 298 228 8.07E−05 0.00521996 0.098
ZEB2 221 298 0.00044122 0.01814406 0.098
TBC1D8 298 267 4.63E−07 9.26E−05 0.098
LEMD3 255 228 4.39E−05 0.00328553 0.098
SLC38A1 229 250 0.00082857 0.02784684 0.098
JARID2 298 298 0.000533 0.02081864 0.097
SLC38A9 256 298 1.03E−05 0.00111287 0.096
AC119396.1 274 298 0.00027994 0.0130508 0.096
UBE3C 254 237 1.32E−07 3.29E−05 0.095
MARCHF8 200 298 1.37E−05 0.00132994 0.095
TUBGCP4 298 284 0.00073663 0.02574939 0.095
SLAMF1 298 239 0.00023608 0.01166772 0.092
GTF2H2 257 213 0.00105913 0.03246645 0.091
IRF8 255 298 0.00017435 0.00929061 0.091
POMZP3 241 287 0.00176872 0.04633317 0.09
MCM6 295 291 0.00111899 0.03391976 0.09
PVT1 260 245 0.00025768 0.01237056 0.09
NIBAN3 298 265 0.00144908 0.04067329 0.09
NFS1 284 298 0.00055428 0.02130244 0.088
KDM3B 224 298 0.00105281 0.03233151 0.088
AC114490.2 298 298 0.0002489 0.01206848 0.088
ZC3H13 261 258 0.00157672 0.04279528 0.088
TGS1 298 267 0.00094666 0.03016446 0.087
CR1 298 298 4.31E−05 0.0032423 0.087
POMZP3 298 267 0.00123126 0.03638696 0.087
POMZP3 298 298 0.00093008 0.02983237 0.087
DDX21 298 269 0.00092869 0.02980962 0.087
SYNE1 298 298 2.82E−06 0.00039618 0.086
ZBTB17 298 275 0.00017027 0.00914048 0.086
MYOM1 298 186 0.00175913 0.04613745 0.085
TIMM23B-AGAP6 219 298 4.87E−06 0.00060876 0.085
SBNO1 285 262 0.00123301 0.03641393 0.084
RAB11FIP3 284 185 8.48E−05 0.00544454 0.084
CNOT1 298 298 0.00118129 0.0353477 0.084
NMRK1 297 221 5.01E−05 0.00365048 0.083
IRF8 197 298 0.00022063 0.01111798 0.083
TSC2 298 262 0.00192466 0.04877674 0.083
RCHY1 228 194 0.00039417 0.01667546 0.083
PVT1 298 245 0.0004551 0.01857509 0.082
COG8 298 298 0.00011458 0.00677684 0.082
FKBP15 234 219 6.52E−06 0.00076584 0.081
PLBD1-AS1 198 298 0.00184072 0.04752409 0.081
TOM1 209 189 0.00020697 0.01062645 0.08
SUGP1 253 298 0.00036801 0.01585242 0.08
MCTP1 259 247 0.0001488 0.00827339 0.08
ZNF185 191 233 0.00028197 0.01310331 0.08
TAF1D 197 184 0.00013431 0.00759342 0.08
CELF1 278 263 0.00078092 0.02680339 0.08
PIGG 298 298 2.92E−05 0.00240459 0.08
C11orf80 298 259 0.00133562 0.03847959 0.079
ZNF638 275 187 0.00013735 0.00772555 0.079
TRIM14 298 242 0.0004024 0.01695619 0.079
NEIL2 289 298 0.0013671 0.03905099 0.078
SNX9 298 297 0.00156255 0.04254252 0.078
NSUN6 269 294 0.00107771 0.03285145 0.078
MRTFA 298 298 0.00083327 0.02794029 0.078
SLC3A2 208 298 2.27E−05 0.00196658 0.077
SNAPC1 298 245 0.00038758 0.01651474 0.077
ING4 221 255 0.00083585 0.02796217 0.077
SERF2 205 201 0.00050539 0.0200273 0.077
FAM114A2 298 249 1.69E−05 0.00155636 0.076
CELF1 278 260 0.0012026 0.03575811 0.076
NFKB2 235 275 0.00089617 0.02913041 0.076
VARS1 274 253 0.00078159 0.02680525 0.074
CLEC17A 245 298 1.59E−08 6.01E−06 0.074
TMEM184B 241 298 0.00103551 0.03206607 0.074
EML2 284 281 0.000151 0.00838483 0.074
CCM2 298 298 0.00022421 0.01125968 0.073
WRNIP1 298 298 0.00108961 0.03312142 0.073
DENND4B 298 285 0.00043357 0.01791425 0.073
AL392172.1 246 220 2.53E−06 0.00036164 0.073
TMEM131 298 292 0.00054011 0.02094966 0.073
RYK 250 275 0.00084547 0.02819757 0.073
TMCO3 298 229 1.54E−05 0.00144515 0.073
FOXP1 219 298 1.92E−05 0.00171489 0.072
DNMT1 278 291 5.58E−05 0.00395965 0.072
ZNF254 276 245 0.00018757 0.00986269 0.072
TCFL5 298 291 0.00147091 0.04110058 0.071
PILRB 247 283 0.00170619 0.04532157 0.071
IDH1 298 298 5.73E−05 0.00403193 0.071
NUP98 298 298 0.00124158 0.03651864 0.071
DDB2 298 292 0.00048574 0.01953283 0.071
IGHD 221 298 0.00034604 0.01522089 0.071
POLR2J3 298 298 3.00E−05 0.00243688 0.07
UBAP2L 217 298 0.00020992 0.01073042 0.07
TSEN2 227 200 2.20E−10 1.85E−07 0.07
COA1 270 250 8.68E−11 8.23E−08 0.07
MPHOSPH6 240 244 0.00193992 0.04896416 0.07
CERS4 256 298 0.00074575 0.02594337 0.07
AC069281.2 211 266 0.00028772 0.01328564 0.069
ATP2B4 298 257 0.00064377 0.02384251 0.069
EIF4G1 298 254 0.00083901 0.02804646 0.069
WDFY3 246 298 0.0007332 0.02565006 0.069
ECPAS 271 298 0.00089734 0.02913442 0.069
SLC25A19 298 298 0.00154334 0.04244113 0.069
STAU2 295 284 0.00021038 0.01073818 0.068
RPS6KA3 231 230 0.00182483 0.04717926 0.068
DUS2 298 237 0.00023172 0.01151709 0.068
MAN1B1 298 298 4.34E−05 0.00325834 0.068
KMT2D 280 298 0.00030157 0.01363622 0.068
RRP8 298 256 0.00142702 0.0403396 0.068
SPAG9 298 263 0.00029058 0.01334711 0.068
CPNE1 204 283 0.00121605 0.03605966 0.067
UBXN11 250 204 0.00015983 0.0087416 0.067
SLC44A2 234 298 0.0001527 0.00844861 0.067
KDM5A 284 255 0.0017128 0.04543138 0.067
TNPO1 245 225 0.00057925 0.0218988 0.067
HEATR5B 298 298 1.12E−05 0.00115495 0.066
RNF170 258 223 0.00135517 0.03880519 0.066
RHOT1 202 251 8.29E−05 0.0053315 0.066
TMEM50B 247 233 0.00034375 0.01515092 0.065
SCLT1 228 245 0.00127582 0.03719944 0.065
MAN2B1 230 298 0.00062591 0.0233192 0.065
PCBP1-AS1 298 246 9.80E−05 0.00602325 0.065
AC069281.2 226 211 0.0001373 0.00772555 0.064
DTNBP1 200 210 0.00131318 0.03800884 0.064
PINK1 298 298 0.00059704 0.02243514 0.064
HDAC7 233 260 7.99E−07 0.00014692 0.064
CMTM1 283 248 0.00050909 0.0201369 0.064
CDC23 269 225 0.00174379 0.04592855 0.064
PCBP1-AS1 298 298 0.0006505 0.02396901 0.064
PCBP1-AS1 298 298 0.00070862 0.02506553 0.064
EHBP1L1 203 298 0.0009658 0.03051008 0.063
ANKZF1 298 298 0.00121385 0.03604339 0.063
AC118553.2 245 212 1.04E−06 0.00018014 0.063
NAE1 213 241 3.00E−05 0.00243688 0.063
GIT1 236 223 0.00037497 0.01607167 0.063
CREBBP 298 298 0.00103022 0.03193966 0.063
RALY 197 298 1.24E−05 0.00124332 0.062
XAF1 298 298 1.26E−08 4.95E−06 0.062
CCM2 298 233 0.00057549 0.02182961 0.062
CPSF7 298 207 6.88E−05 0.00458061 0.062
CAST 230 188 0.00165527 0.04422018 0.062
SMG5 298 298 4.67E−05 0.00344756 0.062
PVT1 262 245 7.86E−05 0.00511519 0.062
RGS6 298 239 0.00044255 0.01818155 0.062
SUMF2 194 298 0.00095616 0.03033397 0.062
RALY 197 298 1.26E−05 0.00125274 0.061
RALY 197 298 1.29E−05 0.00127168 0.061
MLKL 285 231 0.00048689 0.0195609 0.061
ITPA 265 226 6.31E−05 0.00430417 0.061
GATAD2A 239 281 0.00077975 0.0268032 0.061
MKNK1 254 205 0.0010365 0.03206607 0.061
MIR4435-2HG 298 243 0.00118027 0.0353477 0.061
SSBP4 234 239 2.11E−05 0.00184807 0.061
CCM2 298 233 0.00096661 0.03051008 0.06
TNFRSF1A 223 298 0.00065811 0.02414738 0.06
TLE3 298 226 0.0001088 0.00655037 0.06
ARHGAP25 298 237 0.00089763 0.02913442 0.059
TRAK1 298 298 0.00181709 0.04709083 0.059
LRCH3 221 198 0.00169016 0.04503314 0.059
TLE3 298 226 0.00012445 0.0071754 0.059
PLD3 292 298 0.00182639 0.0471916 0.059
ADA 277 221 0.00043265 0.01789317 0.058
SHISA5 265 298 0.00024278 0.01189061 0.058
NCF1 254 295 0.00029681 0.013463 0.058
NUP88 298 275 0.00051554 0.02027376 0.058
USB1 203 255 0.00032957 0.01463688 0.058
FMNL1 298 251 0.0006872 0.02482549 0.058
CYB5R4 182 182 7.92E−05 0.00514256 0.057
NFKB2 288 298 0.00105104 0.03230934 0.057
NUP88 298 298 0.0010677 0.03263743 0.057
RCBTB2 298 257 0.0014398 0.04060637 0.057
STRADA 252 271 0.00042276 0.01758391 0.057
CRTC2 298 298 0.00089401 0.02910375 0.057
UNC13D 242 253 0.00027138 0.01280955 0.057
ICE1 298 298 0.00178031 0.04649707 0.056
TMBIM1 203 200 1.05E−05 0.00112187 0.056
SH2D3C 298 274 0.00020997 0.01073042 0.056
SLC44A2 242 234 0.00041184 0.0172616 0.056
SORL1 298 217 8.62E−05 0.00549336 0.056
LTBR 247 257 0.00153637 0.04227925 0.056
CHP1 277 21 6.70E−05 0.00448333 0.056
CTDNEP1 261 234 0.0005603 0.02140532 0.056
RPS12 252 251 1.94E−05 0.00172366 0.055
WDFY4 298 297 0.0017349 0.04579958 0.055
FANCA 298 258 4.75E−05 0.00349735 0.055
CPNE1 298 283 0.00087971 0.0289142 0.054
CPNE1 283 283 0.00073825 0.0257833 0.054
OSBPL11 298 295 0.00071835 0.02533312 0.054
RHOT1 202 258 0.00064741 0.02392665 0.054
ITGAL 225 263 0.00087182 0.02877966 0.054
INTS8 298 257 0.00141944 0.04017762 0.053
DBNL 198 231 0.00064505 0.02386895 0.053
GSN 283 240 0.00058209 0.02197879 0.053
CNOT3 206 298 0.00029295 0.01339947 0.052
DAGLB 276 227 0.00013979 0.00783195 0.052
DBNL 198 255 0.0006283 0.02338822 0.052
STXBP2 259 245 0.0003417 0.01507544 0.052
SNHG29 298 218 1.38E−06 0.00022001 0.052
UNC13D 255 221 0.0007848 0.02685201 0.052
FCHO1 291 298 0.00067804 0.02459404 0.052
SLC35C2 298 279 0.00151146 0.04186972 0.051
WDR47 298 28 2.15E−07 4.90E−05 0.051
MKNK2 298 298 0.00108304 0.03299074 0.051
INPP5D 298 290 0.00177622 0.04646003 0.051
LRCH4 211 253 0.00093846 0.03005708 0.051
TTC7A 254 267 0.00035511 0.01547905 0.051
UNC93B1 243 274 0.00132996 0.0383674 0.051
PDE4B 298 249 0.00184489 0.04755705 0.051
HLA-DRB1 298 298 3.00E−07 6.47E−05 0.05
TNFRSF1A 178 298 0.00070901 0.02506553 0.05
AC118553.2 283 245 0.0008742 0.02880289 0.05
FGR 298 298 0.00055303 0.02130244 0.05
COG4 251 278 0.00197944 0.04970273 0.05
FLOT1 240 269 0.00107116 0.0326975 −0.05
CAMK1D 225 262 0.00038266 0.01636919 −0.05
LMBR1 230 216 0.00053683 0.02093045 −0.05
TSC2 276 293 6.70E−11 6.49E−08 −0.05
FGR 212 248 1.94E−05 0.00172366 −0.05
NAA60 219 279 4.67E−11 4.73E−08 −0.05
INTS6 210 298 5.78E−07 0.00011104 −0.05
TTC16 291 298 0.00022158 0.01115312 −0.051
H2AZ2 227 279 0.00036803 0.01585242 −0.051
AC004997.1 228 220 1.39E−08 5.32E−06 −0.051
SPTLC1 282 298 0.00072102 0.02536662 −0.051
BAG6 209 29 0.00024165 0.01186215 −0.051
TTC17 298 298 0.00073059 0.02560087 −0.051
CDK16 240 227 0.00150986 0.04186697 −0.051
NAXD 298 195 1.48E−05 0.00140621 −0.051
IGFLR1 298 298 0.00060981 0.02280057 −0.051
GOLGA7 282 298 1.17E−06 0.00019558 −0.052
YY1AP1 190 253 4.95E−08 1.49E−05 −0.052
YY1AP1 190 253 2.74E−08 9.63E−06 −0.052
CASC4 252 230 0.00188468 0.04827725 −0.052
PTDSS1 194 274 0.00061092 0.02281929 −0.052
CEP290 298 272 0.00041501 0.01732787 −0.052
TIMM23B-AGAP6 280 219 3.22E−05 0.00258438 −0.052
IL21R 214 252 0.00013945 0.00782313 −0.052
DNMT1 186 257 0.00010149 0.0061957 −0.052
PDIA4 298 298 0.00012638 0.00723902 −0.053
SIPA1 298 298 0.00126219 0.03690062 −0.053
POLR2F 219 280 0.00181023 0.04698247 −0.053
POLL 298 278 0.00174752 0.04597122 −0.053
PSMA5 216 276 0.00019112 0.01001319 −0.053
PAFAH2 298 298 0.00041279 0.01727535 −0.053
MOV10 298 298 0.00032378 0.01447397 −0.053
HMGB2 298 295 0.00137005 0.03910973 −0.053
PYCR2 220 298 0.00130572 0.03786846 −0.053
B4GALT3 295 298 0.0009858 0.03098116 −0.053
RHOT2 227 272 0.00156139 0.04254252 −0.053
DDX17 29 298 0.00160304 0.04332089 −0.054
NQO2 298 241 0 0 −0.054
WDR70 209 283 0.00085794 0.0284391 −0.054
INTS8 250 291 0.00195612 0.04931592 −0.054
EXOSC1 265 238 0.00055147 0.02129198 −0.054
RABEPK 208 298 7.05E−08 1.97E−05 −0.054
UTP6 231 231 0.00040601 0.01708287 −0.054
TRPC4AP 298 298 0.00020351 0.0104982 −0.055
XAF1 206 235 0.00144628 0.04064685 −0.055
ZDHHC4 298 273 0.00064379 0.02384251 −0.055
PHYKPL 268 266 0.00114423 0.03454075 −0.055
CAST 212 22 0.00133554 0.03847959 −0.055
PPA2 194 236 0.0015332 0.04221873 −0.055
RBM6 239 219 0.00066847 0.02442454 −0.055
DDX21 223 298 0.00066557 0.02434895 −0.055
RCBTB2 292 298 0.00151538 0.04192845 −0.055
ABCA7 281 289 0.0002251 0.0112652 −0.055
LMF2 178 298 8.30E−06 0.00092973 −0.056
PHC2 257 279 0.00111505 0.03384752 −0.056
WDSUB1 183 290 4.05E−06 0.00052126 −0.056
JAK1 232 298 0.00082215 0.02767365 −0.056
IFTAP 298 298 0.00134759 0.03864545 −0.056
RABEPK 298 298 3.56E−10 2.72E−07 −0.056
SNX10 196 236 0.00049787 0.01981726 −0.057
DAGLB 298 272 0.00012302 0.00712155 −0.057
DEK 251 259 0.00187567 0.04817936 −0.057
WDSUB1 243 290 0.00010243 0.00624453 −0.057
LAIR1 185 298 0.00032322 0.0144653 −0.057
VDAC2 218 199 5.50E−06 0.00067116 −0.057
PPP4R3B 248 298 0.00184323 0.04754237 −0.057
DLEU2 228 278 0.0001427 0.00798477 −0.057
STK38 285 201 6.60E−05 0.00444473 −0.057
STAT5B 287 298 0.00157672 0.04279528 −0.057
DESI1 219 259 0.00040756 0.01713186 −0.058
CCM2 298 285 1.11E−05 0.00115158 −0.058
PREX1 221 298 0.00028737 0.01328362 −0.058
TMEM87A 249 243 0.00126932 0.03705946 −0.058
NEPRO 298 298 0.00053956 0.02094966 −0.058
WDR37 298 246 3.99E−07 8.20E−05 −0.058
LAIR1 185 298 0.00029592 0.01345083 −0.058
LAIR1 185 298 0.00031595 0.01419835 −0.058
SUPT20H 208 216 0.00158899 0.04302106 −0.058
CDC16 204 247 0.00104674 0.03224559 −0.058
JPX 298 247 0.00119803 0.03569523 −0.058
RBM23 27 267 3.25E−06 0.00044033 −0.058
RPL18A 298 279 0.00066958 0.0244326 −0.058
LINC00893 298 230 5.96E−10 4.26E−07 −0.059
ZDHHC4 298 273 0.00011885 0.00697279 −0.059
SND1 298 270 0.00179492 0.04671089 −0.059
SLC3A2 298 241 0.00010972 0.00657882 −0.059
RBM33 298 298 4.11E−05 0.0031397 −0.059
TMEM63A 187 292 0.00099706 0.03120015 −0.059
MEF2D 206 298 0.00174503 0.04593336 −0.059
NLRC5 298 233 0.00142567 0.04032756 −0.059
POLD2 298 271 0.00122113 0.03618564 −0.059
TNFSF13 228 268 0.0006477 0.02392665 −0.06
NTAN1 282 223 0.00189266 0.04833099 −0.06
VPS53 216 236 0.00027857 0.01304269 −0.06
TANGO2 298 238 1.92E−06 0.00028707 −0.06
ARHGEF40 298 298 0.00070675 0.02506553 −0.06
ZDHHC24 298 220 0.00184863 0.04758306 −0.06
ABCA7 182 298 0.00094423 0.03016446 −0.06
SAMD9L 297 251 7.31E−06 0.00084266 −0.061
EPSTI1 298 223 0.00039413 0.01667546 −0.061
POLR3C 242 298 0.00022449 0.01126053 −0.061
ECHDC1 298 202 0.00189734 0.04838041 −0.061
GMDS-DT 251 298 5.82E−08 1.74E−05 −0.061
WDSUB1 243 298 9.35E−05 0.00583102 −0.061
TYROBP 182 284 0.00025084 0.01213547 −0.061
TTC13 291 298 0.0010256 0.03186336 −0.061
PHF20L1 298 298 0.00124025 0.03650415 −0.061
CORO1C 298 279 0.0014424 0.04061638 −0.061
ECHDC1 296 202 7.33E−05 0.00479702 −0.062
SMIM8 298 269 1.06E−07 2.80E−05 −0.063
NEPRO 298 270 0.0003125 0.01405763 −0.063
HLA-C 182 197 0.00038413 0.01641601 −0.063
BBS9 290 245 2.87E−05 0.00237292 −0.063
AMD1 236 276 0.00132144 0.03817193 −0.063
ERCC1 249 221 8.87E−05 0.00562885 −0.063
DLG1 298 298 0.00023498 0.01162618 −0.064
ZFAND1 298 27 1.54E−06 0.00024138 −0.064
MAPKAPK5 223 247 0.00151934 0.04194292 −0.064
CELF1 298 293 0.00114354 0.03454075 −0.065
PVT1 264 262 0.0019744 0.04963339 −0.065
WASH3P 298 298 1.18E−05 0.0012005 −0.065
CNOT2 292 272 1.91E−06 0.00028707 −0.065
RFFL 298 298 5.51E−09 2.40E−06 −0.065
LONP2 272 298 2.97E−05 0.00243429 −0.066
ARIH2 217 298 0.00035947 0.01560666 −0.066
SNX22 254 182 0.00018453 0.00973803 −0.067
SCAP 298 235 0.00094253 0.03016446 −0.067
VASP 250 186 0.00124461 0.03658295 −0.067
FKBP15 248 298 0.0007852 0.02685201 −0.067
PSD4 266 225 0.00161595 0.04361577 −0.068
INTS8 298 291 0.000363 0.01572898 −0.068
TANGO2 244 238 4.69E−06 0.00058734 −0.068
TMEM127 298 298 0.00069557 0.02499364 −0.068
LRCH3 203 221 0.00022765 0.01136697 −0.068
KDM5C 227 272 0.0007861 0.02685427 −0.068
BBS1 281 256 4.89E−06 0.00060876 −0.068
SRP14-AS1 298 298 0.00177782 0.04646003 −0.069
SOS1 298 268 0.00127929 0.03724715 −0.069
RNF121 283 261 0.00090561 0.02926942 −0.069
PDCD6 211 259 0.00087283 0.02877966 −0.069
SEC16A 232 298 5.17E−06 0.00063693 −0.069
ADAP2 229 262 3.24E−10 2.54E−07 −0.069
DNAJC2 251 225 0.00180778 0.04698247 −0.07
RPS6KB1 218 297 0.00011991 0.00699306 −0.07
RNF121 283 251 0.0006571 0.02413051 −0.07
CEP290 298 272 0.00187361 0.04815481 −0.07
PVT1 298 262 0.00027267 0.01283561 −0.07
EXOSC9 252 287 0.00077921 0.0268032 −0.07
CLPTM1 262 273 0.00025327 0.01219911 −0.07
PREX1 221 254 0.00088261 0.02893181 −0.071
IL15 298 247 2.01E−06 0.00029751 −0.071
MTA1 243 276 0.00035329 0.01544943 −0.071
EFCAB13 293 293 0.00015383 0.00849893 −0.071
OCEL1 298 203 1.47E−07 3.56E−05 −0.071
ZC3H7A 250 298 3.00E−05 0.00243688 −0.072
DAGLB 230 298 1.11E−16 8.07E−13 −0.072
EIF2B4 298 241 0.00074311 0.0258929 −0.072
EIF2D 298 239 0.00071125 0.02512434 −0.072
GUSBP11 261 262 1.21E−05 0.00122804 −0.073
FBXO3 239 298 0.00069608 0.02499364 −0.073
VASP 250 201 0.00069033 0.02488956 −0.073
GRK3 216 250 0.00080576 0.02729079 −0.073
PIK3AP1 298 286 0.00084136 0.02809443 −0.073
CDC16 204 244 0.00028081 0.01306337 −0.073
RALGAPB 269 228 0.00165704 0.04423183 −0.074
PAPSS1 264 298 0.00011063 0.00660603 −0.074
RABGAP1L 243 298 0.00020998 0.01073042 −0.074
C1orf21 298 244 0.0004357 0.01796803 −0.074
LAIR1 298 200 0.00089099 0.02907056 −0.074
ST6GAL1 281 298 0.00029172 0.01337047 −0.074
OGFOD1 266 241 0.00190074 0.04838041 −0.075
ARAP2 197 289 8.93E−10 5.64E−07 −0.075
FDX1 274 279 0.00193158 0.04883842 −0.075
TTC39B 184 245 0.00133992 0.03857788 −0.075
CD320 298 298 0.00131934 0.03813661 −0.075
RUNX3 298 254 0.00175825 0.04613745 −0.076
COP1 247 226 0.00120909 0.03592659 −0.076
ANKRD27 298 298 0.00067269 0.02447613 −0.076
TXLNA 298 241 0.00021137 0.01077625 −0.076
TPGS2 229 237 0.00027989 0.0130508 −0.076
MCTP1 292 229 0.00173859 0.04584711 −0.077
AD000671.1 179 235 0.00034451 0.01516883 −0.077
COQ7 289 218 3.53E−05 0.00277052 −0.077
NRF1 298 264 0.00037239 0.01597691 −0.077
IFTAP 298 298 1.55E−05 0.00145463 −0.077
SCFD1 240 272 0.00161509 0.04361577 −0.077
LY96 278 202 0.0011815 0.0353477 −0.078
TMCO4 298 177 0.0015068 0.04180873 −0.078
ANKZF1 262 252 0.00020283 0.01047538 −0.078
SCYL1 298 204 0.00101661 0.03167554 −0.078
PTPRA 228 234 0.0006988 0.02501772 −0.079
DRAM1 217 298 0.00042518 0.0176592 −0.079
USP48 283 232 3.92E−06 0.00050756 −0.079
ARHGEF40 230 266 0.00047117 0.01910525 −0.079
CHFR 294 249 4.18E−05 0.00318095 −0.079
GYS1 256 209 0.00050246 0.01992941 −0.079
RORC 298 257 4.60E−08 1.41E−05 −0.08
UVRAG 234 237 0.00116826 0.03513824 −0.08
SIRPB1 298 264 4.88E−07 9.67E−05 −0.08
TTI2 298 298 0.00013362 0.00756404 −0.08
COP1 209 218 0.00134847 0.03864545 −0.081
TMEM8B 228 298 2.02E−07 4.64E−05 −0.081
CAPN12 209 220 0.00018348 0.00970603 −0.081
HIPK3 298 273 0.00189156 0.04833099 −0.081
SRC 226 298 0.00074393 0.02590081 −0.082
HERPUD2 298 298 3.50E−06 0.00046474 −0.082
KLRG1 254 250 0.00030383 0.01372427 −0.082
COP1 247 218 0.00022269 0.01119627 −0.082
WDSUB1 243 256 0.00153258 0.04221873 −0.082
SPG7 289 252 0.00027005 0.01278465 −0.082
P4HA1 220 220 0.00184918 0.04758306 −0.083
IKBKG 268 298 1.24E−09 7.49E−07 −0.083
METTL26 209 217 0.00019291 0.01009501 −0.083
DNAJC1 251 298 0.00166863 0.04451387 −0.083
NACC2 298 298 0.00148703 0.04136536 −0.083
THOC6 214 253 0.0002775 0.01300654 −0.083
ALG13 253 208 5.04E−05 0.00366823 −0.084
RB1 266 181 0.0001852 0.00976185 −0.084
LRP8 272 298 0.00180895 0.04698247 −0.084
BCAS3 283 298 0.00106496 0.03259934 −0.084
RNF170 225 258 0.00089894 0.0291555 −0.085
MDM4 283 205 0.00198866 0.04990405 −0.085
METTL26 209 298 9.09E−05 0.00570301 −0.085
FANCA 223 278 1.53E−05 0.00144217 −0.085
CWF19L1 234 251 0.00020514 0.01055723 −0.085
LRRK2 229 256 8.92E−05 0.00562885 −0.085
PRMT9 298 298 0.00090271 0.02923408 −0.086
NUP54 298 298 0.00035264 0.01544943 −0.086
ANKZF1 298 252 0.00140909 0.04001439 −0.086
NAE1 229 259 1.68E−05 0.00155321 −0.086
PPP2R2D 242 247 0.00124751 0.03661993 −0.087
TSEN2 200 288 1.51E−12 2.19E−09 −0.087
IKBKG 268 298 0.00147604 0.04121753 −0.088
THEM4 298 298 0.00090918 0.02933466 −0.088
COP1 247 218 0.00016503 0.00894743 −0.088
CAST 188 242 0.00097954 0.03082905 −0.089
AGPAT3 212 298 0.00028944 0.01332258 −0.089
TRPM7 214 246 0.0002457 0.01196632 −0.089
RAD1 298 298 0.00069471 0.02498552 −0.09
RNPC3 197 268 0.00131201 0.03800026 −0.09
WDSUB1 183 256 2.72E−05 0.00227432 −0.09
SLBP 254 209 0.00024552 0.01196632 −0.09
KIF1C 270 282 1.46E−05 0.00139182 −0.091
FOXRED1 244 251 2.62E−05 0.00220967 −0.092
DICER1-AS1 191 298 1.17E−10 1.06E−07 −0.092
CRBN 212 234 0.00018808 0.00987763 −0.092
PACC1 292 257 0.00035769 0.01555 −0.093
SPATA13 286 298 0.00021538 0.01091448 −0.093
ABCB7 269 282 0.00191844 0.0487041 −0.094
DENND4B 298 272 0.00049381 0.01972988 −0.094
JAK2 232 298 6.86E−05 0.00458061 −0.095
N4BP2L1 238 226 0.00038747 0.01651474 −0.095
IMMP1L 212 238 2.98E−06 0.0004115 −0.096
TBC1D2B 298 298 0.0016479 0.0442044 −0.096
ATF7IP 298 233 0.00096862 0.03052935 −0.097
SLBP 254 230 9.08E−05 0.0057021 −0.098
ARHGAP19 298 236 0.00012221 0.00709339 −0.098
POLL 298 278 0.00058748 0.02211403 −0.099
IL15 271 260 2.34E−07 5.28E−05 −0.099
RIN3 298 222 0.00053977 0.02094966 −0.099
PXN 298 298 2.77E−05 0.00230546 −0.099
PLXDC1 298 293 0.00022564 0.01127917 −0.099
N4BP2L1 277 226 0.00163752 0.04403428 −0.099
PI4KAP2 250 298 3.39E−06 0.00045189 −0.099
SUZ12P1 196 214 3.26E−14 7.90E−11 −0.099
SCAF8 194 298 0.00012491 0.00718321 −0.1
GTF2IRD2B 288 269 0.0005915 0.02224625 −0.1
SENP6 210 254 0.0016522 0.04422018 −0.101
DNMT3A 298 298 0.00012862 0.00730948 −0.101
DCP1B 190 277 0.00099676 0.03120015 −0.101
TMEM39A 298 233 0.00066584 0.02434895 −0.102
CBWD3 272 298 0.0003886 0.01653813 −0.102
RETSAT 298 269 0.00012069 0.00701945 −0.102
DENND6A 214 239 0.00039441 0.01667546 −0.103
ZSWIM7 263 271 0.00088488 0.02894276 −0.104
AK5 298 298 0.00033047 0.01465444 −0.105
MDM1 264 298 0.00150232 0.04171098 −0.105
ITGA6 229 281 0.00100373 0.03136399 −0.106
HDAC4 298 270 0.00043444 0.01793299 −0.108
SIRPB1 298 298 8.21E−08 2.24E−05 −0.108
ELMO2 228 200 0.00091362 0.02943425 −0.109
ABCA7 298 182 0.00063596 0.02361074 −0.109
HLA-B 298 266 3.86E−06 0.00050187 −0.111
KIAA0753 212 298 0.00068798 0.02482549 −0.111
MRNIP 229 238 0.00057184 0.02176982 −0.111
RIOK1 240 219 0.00081991 0.02761981 −0.111
HLA-B 298 298 4.68E−08 1.42E−05 −0.112
RNF144B 298 254 0.00187716 0.04818926 −0.112
RAB35 200 274 4.90E−05 0.00358265 −0.112
DOCK10 269 239 0.00063491 0.02359385 −0.112
FBXL4 267 298 0.0009662 0.03051008 −0.113
TMEM189-UBE2V1 269 241 0.00134654 0.03864097 −0.114
SEPTIN11 264 298 0.00051596 0.02027376 −0.115
RBM22 203 179 1.13E−05 0.00115495 −0.116
BSCL2 298 231 0.00026261 0.01252435 −0.116
SNHG17 234 298 1.00E−12 1.61E−09 −0.117
SORBS3 289 298 0.00044716 0.01831936 −0.117
SPOPL 287 271 0.00179263 0.04667914 −0.117
SLC7A6 298 275 0.00041005 0.01721963 −0.117
NDRG1 230 185 0.00031194 0.01405763 −0.118
LAIR1 185 298 0.00017114 0.00917576 −0.118
LAIR1 185 298 0.00015273 0.00844861 −0.119
ATL2 298 277 0.00128019 0.03724715 −0.119
SCAF8 233 298 0.00030632 0.01382264 −0.12
AC009061.2 298 246 0.00033755 0.01492256 −0.12
TMCO4 298 177 0.00094567 0.03016446 −0.121
BSCL2 298 231 0.00011789 0.00693877 −0.121
MAPK6 298 294 0.00036117 0.01566509 −0.121
PLSCR3 298 192 0.00049483 0.01974139 −0.122
FOXJ3 251 298 8.50E−08 2.29E−05 −0.124
SLC39A11 298 294 0.0004892 0.01959948 −0.124
PYROXD1 230 269 0.00161977 0.04369174 −0.125
RNF144B 298 294 0.00126505 0.03695957 −0.125
TMEM220 210 273 0.00021375 0.01085943 −0.126
TADA2A 238 222 0.00134462 0.03861135 −0.126
CYRIB 251 195 2.83E−06 0.00039618 −0.127
PEX1 293 233 0.00165522 0.04422018 −0.129
TSPAN2 252 248 0.00032321 0.0144653 −0.129
TTLL12 298 298 7.17E−05 0.00474121 −0.132
TMEM234 208 283 9.00E−07 0.00016147 −0.136
BCL9L 203 25 0.001622 0.04369782 −0.136
AC008073.3 287 218 2.45E−13 5.08E−10 −0.137
GNB4 188 256 0.00086786 0.02868069 −0.138
TSPAN2 252 224 0.00088015 0.0289142 −0.139
TMEM234 208 230 0.00016122 0.00879489 −0.142
ERAP2 281 274 0.00013662 0.00770413 −0.143
ANKRD6 248 248 0.0018827 0.04827458 −0.144
DDX60L 298 298 2.02E−08 7.45E−06 −0.147
GTF2H2B 237 257 3.38E−07 7.18E−05 −0.148
SLC35F2 298 202 0.00104997 0.03230339 −0.148
TBCD 247 251 5.79E−05 0.00407092 −0.149
ZFR 298 294 0.00189196 0.04833099 −0.156
PXYLP1 281 298 6.15E−05 0.00424162 −0.158
SOS1 275 281 8.02E−06 0.00090772 −0.16
SNHG17 267 298 0.00088276 0.02893181 −0.164
CA5B 245 229 0.00028838 0.01330213 −0.168
SNHG17 267 298 6.29E−05 0.00429436 −0.171
ERC1 281 298 0.00148698 0.04136536 −0.175
CYRIB 251 195 5.35E−05 0.00385796 −0.176
RANBP10 261 202 1.39E−05 0.00134185 −0.183
AC092070.2 229 276 0.00081014 0.02737517 −0.187
SETD6 298 270 0.00048118 0.01943914 −0.2
ITGB2 210 238 1.28E−08 4.97E−06 −0.209
CEP170 276 246 0.00175625 0.0461252 −0.21
SNHG17 227 298 0.00023949 0.01180907 −0.221
LRP8 298 289 4.05E−05 0.0031146 −0.225
SNHG17 227 298 9.64E−05 0.00595458 −0.233
ANKRD36B 291 298 0.00016386 0.00889504 −0.254
TABLE 19
A3SS_FXSvsTD
GeneID chr strand longExonStart_0base longExonEnd PValue FDR IncLevelDifference
PATZ1 chr22 − 31328786 31328924 0.00025746 0.00975747 −0.093
TPTEP1 chr22 + 16647604 16647785 0.00139658 0.03495258 −0.149
PABPC1L chr20 + 44933056 44933185 1.94E−07 3.31E−05 0.079
SNHG17 chr20 − 38421005 38422368 0.00023295 0.00885665 −0.17
CPNE1 chr20 − 35626566 35626803 3.72E−07 5.77E−05 −0.086
CPNE1 chr20 − 35626566 35626826 1.32E−06 0.00015625 −0.12
ZNF160 chr19 − 53091412 53091529 1.67E−08 4.89E−06 −0.052
XAF1 chr17 + 6759255 6759718 2.15E−08 5.85E−06 0.084
LSM7 chr19 − 2324124 2324196 0.0004093 0.01372545 −0.055
POLR2J3 chr7 − 102543524 102543702 6.03E−05 0.00325599 0.252
TSNARE1 chr8 − 142315002 142315092 0.00127149 0.03292635 0.089
THADA chr2 − 43551788 43551925 6.89E−14 1.37E−10 −0.065
TRIM73 chr7 + 75405181 75405605 6.33E−09 2.52E−06 −0.149
AEBP1 chr7 + 44109656 44110124 3.25E−08 7.61E−06 0.068
TBC1D7 chr6 − 13326786 13326963 0.00161522 0.03864227 0.117
DDX60L chr4 − 168395958 168396127 2.77E−08 6.74E−06 −0.204
ASNS chr7 − 97854579 97854754 9.99E−05 0.00451674 0.062
MTSS1 chr8 − 124556231 124556405 0.00060128 0.01859606 0.1
MZB1 chr5 − 139388460 139388667 3.46E−05 0.00205267 0.052
SEPTIN8 chr5 − 132763705 132763892 7.91E−06 0.00061701 0.134
PPWD1 chr5 + 65569631 65569732 0.00141214 0.03512102 0.062
TMEM116 chr12 − 111932585 111932731 3.98E−05 0.00229594 0.097
TMEM116 chr12 − 111933885 111936830 8.69E−06 0.00065975 0.118
BRD9 chr5 − 889586 889766 8.61E−06 0.00065881 0.062
SDHA chr5 + 254357 254506 0.00213689 0.04777197 −0.156
IKBKG chrX + 154558531 154558650 8.24E−05 0.00393314 −0.118
ZNF707 chr8 + 143691596 143691713 0.00019848 0.00779409 0.104
CEP131 chr17 − 81191192 81191350 0.00028481 0.01042946 0.103
DXO chr6 − 31970342 31970478 3.22E−07 5.27E−05 −0.054
TAFA2 chr12 − 62258762 62258910 0.00132443 0.03378436 −0.102
TPRG1 chr3 + 189150655 189151136 8.85E−06 0.00066422 0.07
DLG1 chr3 − 197076585 197076685 0.00145615 0.03592374 −0.092
GGT1 chr22 + 24627409 24627619 0.00063066 0.01930477 0.059
SRGAP2 chr1 + 206401420 206401645 3.54E−05 0.00207054 −0.203
TMEM161B- chr5 + 88287435 88287622 2.70E−07 4.47E−05 0.062
AS1
HLA-C chr6 − 31269492 31269543 3.39E−08 7.78E−06 0.056
CCDC163 chr1 − 45495417 45495545 0.00136754 0.03458837 0.105
NABP1 chr2 + 191683289 191683804 0.00173822 0.04076781 0.093
RNF181 chr2 + 85596952 85597178 2.72E−05 0.00169037 −0.101
CENPT chr16 − 67828473 67828605 0.00025869 0.00977295 0.061
KHDC4 chr1 − 155916624 155916737 0.00171796 0.040372 −0.066
ZNF7 chr8 + 144837390 144837507 2.62E−08 6.74E−06 0.068
DCAF11 chr14 + 24115514 24115726 0.00153675 0.03706217 0.106
AK5 chr1 + 77293792 77293960 0.00155273 0.03737185 −0.074
ARRB2 chr17 + 4715150 4715336 0.00120351 0.03130181 0.091
ARHGAP25 chr2 + 68807272 68807480 0.00100499 0.02745428 0.081
AHSA2P chr2 + 61178980 61179171 1.21E−05 0.00086042 −0.056
AZIN1 chr8 − 102849998 102850165 5.32E−06 0.0004736 0.056
ZNF540 chr19 + 37601006 37601105 0.00117877 0.03072519 −0.095
MFSD9 chr2 − 102723699 102723909 2.27E−06 0.0002421 −0.061
JKAMP chr14 + 59486712 59486804 0.00199134 0.04528113 0.058
HARS2 chr5 + 140693490 140693665 0.00183476 0.04253071 0.065
RNF32 chr7 + 156676294 156677130 2.11E−06 0.00022679 0.054
BPHL chr6 + 3138040 3140509 0.00093256 0.02612624 0.068
PPP6R3 chr11 + 68587797 68588024 1.58E−11 1.45E−08 −0.052
PPP6R3 chr11 + 68587944 68588024 1.38E−11 1.37E−08 −0.066
HELB chr12 + 66324906 66325126 6.89E−06 0.00055934 −0.058
GALT chr9 + 34648047 34648171 1.40E−05 0.00097725 0.131
ALAD chr9 − 113393446 113393634 0.00135144 0.03432669 0.053
LAIR1 chr19 − 54364294 54364486 0.00015155 0.00628201 0.053
LAIR1 chr19 − 54364294 54364486 0.00058777 0.01832059 0.058
AC016394.2 chr10 + 73253800 73254349 5.90E−05 0.00321776 0.187
CTSB chr8 − 11867253 11867526 1.02E−08 3.59E−06 0.105
NAP1L4 chr11 − 2989128 2989271 5.70E−07 7.73E−05 0.067
ZNF195 chr11 − 3361742 3368855 1.89E−05 0.00124681 0.147
TCTN1 chr12 + 110628766 110628918 0.00016797 0.00679743 −0.067
PHB2 chr12 − 6969955 6970068 3.96E−06 0.00038479 −0.154
PHF1 chr6 + 33415234 33415329 4.42E−06 0.00041542 −0.101
ATG16L2 chr11 + 72821198 72821741 0.00066749 0.02012249 0.07
TMEM25 chr11 + 118532149 118532461 0.00073253 0.02138132 −0.056
SPSB2 chr12 − 6872237 6872997 0.00076683 0.02221956 0.097
YAF2 chr12 − 42210547 42210680 9.65E−05 0.0044638 −0.067
MAP3K12 chr12 − 53486946 53487155 6.24E−10 3.10E−07 0.149
ATXN2 chr12 − 111510384 111510582 0.00010536 0.00469336 −0.059
ARL6IP4 chr12 + 122981570 122981879 2.03E−07 3.41E−05 0.059
TMEM273 chr10 − 49165204 49165361 0.00146171 0.03597907 −0.064
MPP5 chr14 + 67279017 67279537 3.14E−10 1.63E−07 0.078
ALDH6A1 chr14 − 74071194 74071660 0.00067898 0.02040466 0.087
LTK chr15 − 41508068 41508236 2.79E−06 0.0002818 −0.065
FAM219B chr15 − 74904981 74905059 5.18E−06 0.00047073 0.134
MAN2A2 chr15 + 90911366 90911550 0.00069732 0.0206644 −0.053
PSTPIP1 chr15 + 77027799 77027914 0.00080743 0.02322665 0.081
ZNF23 chr16 − 71447596 71449885 1.15E−05 0.00082499 0.054
SPG7 chr16 + 89548979 89549336 3.10E−08 7.39E−06 0.108
GABBR1 chr6 − 29629086 29629247 0.00059447 0.01846376 0.072
MLX chr17 + 42569203 42569606 1.89E−15 4.51E−12 0.064
BRCA1 chr17 − 43076487 43076614 2.10E−05 0.0013478 0.233
TSPOAP1- chr17 + 58351734 58351914 6.16E−05 0.00330253 −0.108
AS1
DPH2 chr1 + 43970905 43971189 0.00114495 0.03010664 0.08
MPPE1 chr18 − 11885675 11885912 0.00047539 0.01559111 0.073
CCDC191 chr3 − 114042702 114042846 6.39E−08 1.39E−05 −0.065
PCBP1-AS1 chr2 − 70048777 70050252 0.00149611 0.03637583 0.083
PCBP1-AS1 chr2 − 70053730 70053812 0.000231 0.00885665 0.067
PCBP1-AS1 chr2 − 70053730 70053815 0.00045916 0.01518421 0.061
VPS33B chr15 − 91016962 91017064 3.16E−06 0.00031467 −0.053
UNC50 chr2 + 98618145 98618515 5.88E−05 0.00321776 −0.083
ZNF345 chr19 + 36851727 36851904 4.12E−05 0.00235209 0.105
TABLE 20
A5SS_FXSvsTD
GeneID chr strand longExonStart_0base longExonEnd PValue FDR IncLevelDifference
PQBP1 chrX + 48897911 48898093 1.81E−06 0.00019968 −0.203
PIGT chr20 + 45416516 45418979 0.00059641 0.02023817 −0.057
TTPAL chr20 + 44484336 44484530 0.00052122 0.01860505 −0.05
FNTA chr8 + 43077215 43080441 2.52E−05 0.00166816 −0.075
NEIL2 chr8 + 11769709 11770335 0.00039292 0.01516544 0.181
CEP152 chr15 − 48741600 48741704 0 0 0.063
DEPDC5 chr22 + 31797599 31797703 1.88E−09 9.00E−07 −0.076
HLA-DMA chr6 − 32949270 32949399 3.71E−06 0.00034707 −0.055
MICA chr6 + 31399783 31400783 0.00057334 0.01978835 0.103
MSTO1 chr1 + 155611215 155611355 4.27E−07 6.33E−05 −0.068
MSTO1 chr1 + 155611215 155611355 5.95E−05 0.00350918 0.056
MSTO1 chr1 + 155613656 155613766 0.00143232 0.04097644 −0.153
ERAP2 chr5 + 96909579 96909809 1.80E−05 0.00136676 0.094
PARP2 chr14 + 20344931 20345126 2.07E−05 0.00149022 0.161
ZSCAN25 chr7 + 99619560 99621574 4.73E−07 6.88E−05 −0.089
HAGHL chr16 + 728115 728424 0.00107855 0.03289787 −0.072
BUD31 chr7 + 99408968 99409245 0.00031267 0.0126686 0.095
FCRL1 chr1 − 157797680 157797820 0.0005073 0.01836214 0.139
AL392172.1 chr1 + 222836995 222837090 0.00036831 0.01442067 0.166
NDUFV2 chr18 + 9124873 9124996 2.27E−12 3.08E−09 0.063
ERVK13-1 chr16 − 2671023 2672570 1.53E−07 3.06E−05 0.061
ERVK13-1 chr16 − 2671344 2672570 3.84E−07 5.79E−05 0.061
APTR chr7 − 77695895 77696255 0.00076843 0.02493262 −0.057
KLRD1 chr12 + 10311463 10311619 1.49E−05 0.00116929 −0.057
IRF3 chr19 − 49665483 49665857 0.00024168 0.01060085 0.102
CUL7 chr6 − 43046510 43047107 0.00164534 0.04549124 −0.104
ZDHHC3 chr3 − 44959126 44959460 6.47E−07 9.09E−05 −0.198
ZDHHC3 chr3 − 44959126 44959460 0.00129914 0.03792196 0.204
RBIS chr8 − 85219235 85219363 0.00120913 0.03607004 0.181
PCBP4 chr3 − 51961748 51962088 0.00127596 0.0374347 0.113
ATP5F1A chr18 − 46094979 46095131 9.62E−08 2.30E−05 0.063
LUCAT1 chr5 − 91313961 91314404 0.00047925 0.01758106 0.073
CCDC14 chr3 − 123946802 123947319 0.00045948 0.01700894 0.052
UBE2I chr16 + 1312346 1312603 2.00E−05 0.00145726 −0.155
ELOA-AS1 chr1 − 23772267 23772426 0.00160251 0.04469475 0.177
SLC25A37 chr8 + 23566107 23566813 8.74E−05 0.00484387 0.058
AGA chr4 − 177436275 177436351 0.00063198 0.02118043 −0.062
CNBP chr3 − 129171651 129171771 6.98E−08 1.78E−05 −0.059
PPIEL chr1 − 39529015 39529164 1.31E−05 0.0010346 0.066
AC022400.7 chr10 − 73801339 73802776 0.00106853 0.03271456 0.073
MRPL43 chr10 − 100986686 100986975 1.19E−09 6.58E−07 −0.142
MRPL43 chr10 − 100986686 100986975 2.63E−06 0.00026084 −0.108
SERGEF chr11 − 18010070 18010139 9.45E−05 0.00520023 −0.159
STAT2 chr12 − 56349344 56349509 7.15E−05 0.0041026 0.053
ULK3 chr15 − 74837750 74837798 1.85E−07 3.42E−05 −0.216
SLC6A12 chr12 − 209772 210043 3.17E−05 0.00205171 0.131
ANXA2 chr15 − 60396150 60396427 0.00021158 0.00976282 0.125
ITGB7 chr12 − 53201117 53201194 3.57E−12 3.68E−09 0.07
TM6SF1 chr15 + 83119577 83119734 0.00024211 0.01060085 0.059
ARL6IP4 chr12 + 122981128 122981299 2.53E−06 0.00025747 −0.052
DDX51 chr12 − 132141102 132141420 1.26E−06 0.0001579 0.081
UBAC2- chr13 − 99200365 99200710 1.22E−05 0.00098372 −0.1
AS1
PXN-AS1 chr12 + 120206544 120206712 0.00017269 0.0083217 0.058
APEX1 chr14 + 20455577 20455773 0.0001489 0.00748522 0.074
NEK3 chr13 − 52143914 52143987 8.80E−09 3.26E−06 0.277
NEK3 chr13 − 52143914 52143987 1.92E−05 0.00142168 0.251
TPM1 chr15 + 63060868 63061273 3.76E−06 0.00034791 0.066
SMPD1 chr11 + 6391383 6392196 3.02E−07 5.03E−05 0.06
UBC chr12 − 124913320 124913774 1.50E−07 3.06E−05 −0.053
DVL2 chr17 − 7230045 7230155 1.45E−06 0.00017071 0.119
DPH2 chr1 + 43970595 43970817 0.00138759 0.04007282 0.083
AC243960.1 chr19 + 41551179 41551494 3.62E−12 3.68E−09 0.065
TABLE 21
RI_FXSvsTD
GeneID chr strand riExonStart_0base riExonEnd PValue FDR IncLevelDifference
GPATCH4 chr1 − 156596080 156596478 0.0019027 0.01963858 0.193
CAPN3 chr15 + 42409930 42410496 0.00478108 0.03931402 0.177
SUN1 chr7 + 852608 852952 8.12E−05 0.00164027 0.174
ZNF7 chr8 + 144829042 144829604 0.00314975 0.0295129 0.166
ATAT1 chr6 + 30645894 30646109 5.97E−05 0.00129679 0.163
PER1 chr17 − 8146896 8147381 0.00140278 0.01570375 0.162
MSTO1 chr1 + 155611215 155611603 0.0001029 0.00195911 0.158
DHRS4L2 chr14 + 24000862 24001084 0.00022375 0.00366117 0.158
RELA-DT chr11 + 65663426 65665543 0.00238179 0.02353446 0.154
TM7SF2 chr11 + 65112810 65113414 3.92E−06 0.00012959 0.154
DERL3 chr22 − 23834502 23837154 0.00111055 0.01306862 0.148
ASB16-AS1 chr17 − 44181622 44183093 0.00548944 0.04382915 0.148
FAN1 chr15 + 30925788 30928656 0.00248416 0.02434479 0.147
ZFC3H1 chr12 − 71656342 71657301 3.74E−08 2.98E−06 0.139
NRBP2 chr8 − 143839508 143839825 0.00367966 0.03306421 0.137
OGFOD2 chr12 + 122975810 122976767 6.82E−05 0.00142008 0.137
SUN1 chr7 + 852608 852952 2.27E−05 0.00056537 0.133
AAAS chr12 − 53315093 53315782 0.00404198 0.03496806 0.127
LILRA1 chr19 + 54594196 54594476 0.0033528 0.03102633 0.127
BPHL chr6 + 3138040 3140509 9.52E−05 0.00185296 0.125
DDX51 chr12 − 132140830 132141420 6.79E−08 4.78E−06 0.123
ZNF266 chr19 − 9418761 9419299 1.61E−09 2.29E−07 0.118
WDR54 chr2 + 74423318 74423982 5.76E−08 4.30E−06 0.117
BCS1L chr2 + 218662196 218662679 0.00293925 0.02793454 0.116
FCSK chr16 + 70466881 70467471 5.73E−05 0.00125974 0.115
SEC31B chr10 − 100505360 100506201 1.22E−05 0.00034557 0.114
POLG chr15 − 89317938 89318749 2.16E−05 0.0005451 0.114
CD3E chr11 + 118312152 118313874 6.25E−09 7.17E−07 0.113
CD19 chr16 + 28932345 28933114 0.00108799 0.01282845 0.113
TUBGCP4 chr15 + 43401715 43403799 0.00575984 0.04548526 0.112
AVIL chr12 − 57807330 57807727 0.00021838 0.00359632 0.111
ZNF160 chr19 − 53091412 53091720 0.00300071 0.02833848 0.108
MINK1 chr17 + 4889646 4890735 0.00204261 0.02078327 0.108
TTC16 chr9 + 127724119 127724897 0.00531007 0.04271109 0.105
ING4 chr12 − 6652661 6653050 0.0001088 0.00204534 0.105
FCGR2B chr1 + 161673959 161677365 3.97E−05 0.00091656 0.102
GINS4 chr8 + 41541808 41545030 0.00049979 0.00677488 0.098
C1R chr12 − 7091451 7092441 1.81E−12 9.01E−10 0.097
TRIM27 chr6 − 28903001 28908840 1.44E−06 5.66E−05 0.097
RABEPK chr9 + 125200541 125200906 0.00202431 0.02066921 0.096
CTC1 chr17 − 8229141 8229446 2.68E−05 0.00065908 0.093
MAN2C1 chr15 − 75359058 75359425 0.00034973 0.0050993 0.091
RASGRP4 chr19 − 38419859 38420262 0.00279479 0.02686051 0.09
WDR24 chr16 − 685868 686186 0.00536989 0.04299383 0.088
RINL chr19 − 38876330 38876781 0.00332881 0.03085216 0.087
ZSCAN25 chr7 + 99619560 99621574 0.00151166 0.01661155 0.086
OGFOD2 chr12 + 122975810 122976767 1.95E−06 7.14E−05 0.086
C1orf174 chr1 − 3890568 3892996 0.00276344 0.02668211 0.085
PAXX chr9 + 136992639 136992974 0.003216 0.02999259 0.081
LINC01128 chr1 + 851926 852766 1.72E−06 6.51E−05 0.08
PRICKLE3 chrX − 49177992 49178475 0.00019694 0.00331628 0.078
IRF3 chr19 − 49664673 49665857 3.28E−06 0.00011384 0.078
MUTYH chr1 − 45332762 45333324 2.15E−10 4.94E−08 0.077
FAHD2A chr2 + 95410526 95411026 1.55E−05 0.00042512 0.075
RIOK1 chr6 + 7402602 7402897 0.00164758 0.0177605 0.074
ZC3H14 chr14 + 88609266 88609803 0.00024537 0.00388056 0.074
TMEM208 chr16 + 67228796 67229278 7.49E−10 1.18E−07 0.074
HARS2 chr5 + 140693490 140693665 6.43E−07 3.03E−05 0.073
MAP4K2 chr11 − 64791908 64792422 0.00106376 0.01267351 0.072
WDR6 chr3 + 49011634 49014293 0.00060222 0.00794777 0.071
ZNF649 chr19 − 51899797 51900294 2.34E−08 2.06E−06 0.07
NEPRO chr3 − 113012733 113013403 5.38E−07 2.60E−05 0.07
BEST1 chr11 + 61959891 61962893 4.53E−06 0.00014591 0.07
THOC6 chr16 + 3025923 3026288 0 0 0.069
PFKM chr12 + 48134942 48135383 0.00071197 0.00915305 0.069
ADA chr20 − 44622828 44623078 4.54E−05 0.00103647 0.068
IFT43 chr14 + 76082294 76082692 1.97E−05 0.00050797 0.067
PPIE chr1 + 39741894 39743297 0.00287993 0.02745813 0.065
BTN3A3 chr6 + 26443956 26445985 0.00184582 0.01925713 0.064
SAMD9L chr7 − 93145384 93146040 0.00556426 0.04423294 0.062
MPPE1 chr18 − 11886498 11886778 0.00210294 0.02124996 0.062
IFFO1 chr12 − 6548064 6548545 0.00345324 0.03171044 0.061
NAGK chr2 + 71068649 71070586 0.00204834 0.02078939 0.06
CCDC159 chr19 + 11353450 11353874 0.00085438 0.01055261 0.06
SAP30BP chr17 + 75705610 75706092 0.00126274 0.01451666 0.059
MRNIP chr5 − 179837275 179840959 0.00332081 0.03082575 0.059
ARHGAP9 chr12 − 57476589 57476963 1.26E−07 8.02E−06 0.059
XPOT chr12 + 64425037 64425457 0.00082895 0.01033549 0.058
P3H1 chr1 − 42746374 42747412 0.00012633 0.00230957 0.058
REC8 chr14 + 24172898 24173198 0.00028464 0.00440822 0.057
SCML4 chr6 − 107744948 107746889 0.00017617 0.00301757 0.056
APEX1 chr14 + 20455225 20455703 0.00023697 0.00381833 0.056
ENDOV chr17 + 80415452 80415821 0.00366074 0.03305725 0.056
HMBS chr11 + 119092124 119092523 5.26E−05 0.00117316 0.055
BRPF1 chr3 + 9745572 9745930 0.00157081 0.01710441 0.055
DHRS1 chr14 − 24292183 24292784 2.94E−05 0.00071464 0.054
NPHP3 chr3 − 132684553 132686387 0.00128041 0.0146074 0.054
KLF4 chr9 − 107487027 107488267 7.52E−14 6.42E−11 0.054
CALCOCO1 chr12 − 53713700 53714241 0.00180502 0.01893054 0.054
RPAIN chr17 + 5425970 5428211 3.43E−07 1.79E−05 0.054
CIRBP chr19 + 1271980 1274440 0.00092856 0.01130533 0.053
KRIT1 chr7 − 92235402 92236542 0.0031679 0.0296365 0.053
BSDC1 chr1 − 32394079 32394425 9.98E−05 0.0019249 0.053
GALT chr9 + 34648333 34648894 0.00071067 0.00915305 0.053
TMEM150A chr2 − 85601020 85601482 0.0017761 0.01869283 0.053
ZSWIM8 chr10 + 73794146 73794639 0.00220143 0.02211789 0.052
DPH1 chr17 + 2040217 2040605 0.00490181 0.03997685 0.052
TMEM205 chr19 − 11345519 11346268 1.23E−05 0.00034559 0.052
CARD8 chr19 − 48232452 48234543 0.00069379 0.00897719 0.051
LFNG chr7 + 2525218 2525567 5.96E−08 4.35E−06 0.051
NDUFAF7 chr2 + 37241577 37242693 0.00032606 0.00484879 0.051
ARGLU1 chr13 − 106557047 106559657 4.99E−06 0.00015788 0.051
RNF44 chr5 − 176529730 176530206 3.42E−05 0.00081234 0.05
NRBP2 chr8 − 143835819 143836030 1.42E−06 5.66E−05 0.05
ERVK13-1 chr16 − 2669410 2672570 2.29E−06 8.31E−05 0.05
ZNF7 chr8 + 144829042 144829604 1.14E−07 7.47E−06 −0.05
MSTO1 chr1 + 155611215 155611603 4.87E−05 0.00110649 −0.052
MIB2 chr1 + 1628272 1628722 1.27E−05 0.00035643 −0.055
TMEM147 chr19 + 35546671 35547240 0.0001275 0.00232369 −0.055
BBS1 chr11 + 66515539 66515731 0.00033646 0.00494192 −0.057
ZNF160 chr19 − 53091412 53091720 4.30E−11 1.11E−08 −0.058
ZNF577 chr19 − 51886820 51887936 2.03E−05 0.00052052 −0.059
MFSD2A chr1 + 39967627 39967916 0.00034008 0.00498285 −0.064
VPS11 chr11 + 119078172 119078997 2.56E−08 2.21E−06 −0.064
PPOX chr1 + 161170906 161171181 0.0063269 0.04924767 −0.065
CDK16 chrX + 47225964 47226703 0.00034662 0.00506624 −0.069
MIB2 chr1 + 1625545 1626754 0.00490882 0.03997944 −0.074
PRPF40B chr12 + 49642234 49642675 0.00182504 0.01909004 −0.079
STARD5 chr15 − 81322407 81324141 1.83E−06 6.84E−05 −0.083
MIB2 chr1 + 1626836 1627207 1.48E−07 9.09E−06 −0.085
CDK16 chrX + 47226993 47227223 0.001357 0.01521984 −0.085
ALG9 chr11 − 111782194 111786520 7.34E−05 0.00150848 −0.089
PPIEL chr1 − 39547578 39548951 0.00030855 0.00466963 −0.099
HTRA2 chr2 + 74531338 74531702 0.00282866 0.02709895 −0.113
MAN2C1 chr15 − 75358461 75358808 0.00237556 0.02353446 −0.124
ZNF528- chr19 − 52396609 52397267 1.36E−05 0.00038005 −0.131
AS1
MYO1G chr7 − 44972114 44975227 0.00166505 0.01780618 −0.16
PHYHD1 chr9 + 128941444 128942038 0.00127981 0.0146074 −0.162
SNHG17 chr20 − 38421005 38422241 6.79E−05 0.00141902 −0.165
TCL6 chr14 + 95668125 95669617 2.48E−05 0.0006141 −0.167
NMRK1 chr9 − 75068995 75070042 3.94E−10 6.90E−08 −0.264
TABLE 22
CARRIER_VS_TD_SE
geneSymbol chr strand exonStart_0base exonEnd PValue FDR type
EXOC7 chr17 − 76091142 76091235 9.34E−09 8.57E−06 UP
LRRC23 chr12 + 6909889 6910026 0.00032136 0.01394753 DN
TPD52L1 chr6 + 125252021 125252036 5.23E−05 0.00421507 UP
NRBP1 chr2 + 27435722 27435746 0.00064854 0.02084914 DN
COX5A chr15 − 74926765 74926887 0.00096182 0.02686428 NC
UBE2Q2 chr15 + 75859877 75859982 0.00052428 0.01842707 UP
SAT2 chr17 − 7626942 7627044 1.38E−09 2.26E−06 DN
ABLIM1 chr10 − 114447879 114448026 0.00118326 0.03071357 DN
TTC3 chr21 + 37150819 37150884 0.00080955 0.02389588 NC
SZRD1 chr1 + 16391374 16391424 0.00013927 0.00836857 UP
KIF21A chr12 − 39346465 39346504 0.00050149 0.01792614 UP
CDC16 chr13 − 114261886 114261948 0.00069299 0.02167629 UP
PRPF38B chr1 + 108693589 108693642 0.00224369 0.04603797 UP
MOBP chr3 + 39499466 39499532 0.00115894 0.03026943 UP
ZNF148 chr3 − 125314936 125315053 0.00137804 0.0337425 UP
GAB1 chr4 + 143457679 143457769 0.00064841 0.02084914 DN
PCDHGC3 chr5 + 141478393 141478546 0.00022554 0.01127053 DN
ZFAND5 chr9 − 72363469 72363606 0.00042095 0.0161939 UP
SGIP1 chr1 + 66695433 66695493 0.00098237 0.02725673 UP
LRRC75A- chr17 + 16439527 16439703 8.35E−09 7.91E−06 DN
AS1
LRRC75A- chr17 + 16439580 16439703 9.84E−10 1.81E−06 DN
AS1
LRRC75A- chr17 + 16439659 16439703 6.77E−07 0.00019304 NC
AS1
PCBP4 chr3 − 51962809 51962892 1.87E−07 8.09E−05 UP
CAMK2A chr5 − 150239703 150239736 8.02E−05 0.00557276 DN
CWC27 chr5 + 64977134 64977238 0.00191753 0.04167371 DN
ARPP21 chr3 + 35717297 35717357 4.58E−06 0.00087943 UP
LSM14A chr19 + 34226407 34226464 2.33E−05 0.0025537 UP
PCBP2 chr12 + 53467804 53467843 0.00033827 0.01426026 UP
ARHGAP26 chr5 + 143207197 143207473 0.0024596 0.04885996 DN
IDH3B chr20 − 2658758 2658837 0.00056708 0.01932662 UP
NOVA1 chr14 − 26472319 26472391 0.00174589 0.03927977 DN
LINC-PINT chr7 − 130959868 130959970 0.00130581 0.03270973 UP
ZNF207 chr17 + 32366664 32366757 1.22E−06 0.00030003 DN
GKAP1 chr9 − 83768817 83768970 0.00202314 0.043108 DN
CDC42BPA chr1 − 227112670 227112913 0.00072056 0.02216975 UP
MAP7D1 chr1 + 36174897 36175008 0.00042274 0.01621597 DN
PAQR6 chr1 − 156245534 156245661 0.00037187 0.01523943 UP
MADD chr11 + 47288967 47289027 0.00155148 0.0363534 DN
MADD chr11 + 47308979 47309042 0.00143511 0.03453551 UP
KIF13A chr6 − 17789871 17789910 0.00014729 0.00865225 UP
UNC79 chr14 + 93634520 93634637 0.00035917 0.01484301 DN
NCAM1 chr11 + 113236300 113236315 2.97E−05 0.00293482 DN
NCAM1 chr11 + 113246367 113246370 0.00119711 0.03080089 DN
CAMK2D chr4 − 113502935 113502977 0.00178425 0.03972543 DN
TRIM33 chr1 − 114397939 114397990 0.00215217 0.04488091 UP
CCAR1 chr10 + 68756272 68756483 8.10E−05 0.0056135 DN
RP5- chr22 + 40364879 40365056 0.00198136 0.04248854 DN
1042K10.14
CAPN3 chr15 + 42408210 42408324 0.00022642 0.01127607 UP
HSD11B1L chr19 + 5686415 5686527 0.00179896 0.03992359 DN
UQCRH chr1 + 46309100 46309127 2.30E−11 2.25E−07 UP
MARK2 chr11 + 63908259 63908304 0.0001404 0.00840188 UP
BIN1 chr2 − 127051153 127051243 0.00149082 0.03549823 NC
AIFM3 chr22 + 20980746 20980767 3.67E−06 0.00077479 DN
COG1 chr17 + 73207701 73207739 2.82E−07 0.00011036 UP
SORBS1 chr10 − 95414493 95414862 0.00180639 0.04002812 DN
BAZ2B chr2 − 159400598 159400664 0.00109098 0.0290259 NC
BRSK2 chr11 + 1459191 1459239 0.0005302 0.01852433 DN
ARMC10 chr7 + 103092476 103092653 0.00039015 0.01563491 DN
AC005154.6 chr7 − 30552099 30552179 0.00057621 0.01942803 UP
LCMT1 chr16 + 25161101 25161204 0.00013305 0.00807714 UP
USMG5 chr10 − 103394198 103394394 2.73E−06 0.00059877 UP
USMG5 chr10 − 103394198 103394394 1.35E−08 1.05E−05 NC
CLSTN1 chr1 − 9737497 9737554 0.00093918 0.02646864 NC
ZMIZ2 chr7 + 44760150 44760228 0.00028376 0.01304811 UP
UQCRB chr8 − 96231378 96231515 4.33E−08 2.60E−05 NC
SH3GLB2 chr9 − 129021090 129021219 0.00242444 0.04832932 DN
CAMK2G chr10 − 73825278 73825347 0.00199683 0.04266565 UP
CAMK2G chr10 − 73828088 73828121 0.00067016 0.0212065 DN
CAMK2G chr10 − 73828088 73828121 0.00212556 0.04445219 DN
ACBD4 chr17 + 45137018 45137139 0.00069627 0.0216951 DN
GPM6B chrX − 13807649 13807769 9.76E−06 0.00139273 UP
MTDH chr8 + 97699753 97699852 0.00028272 0.01303802 DN
MTDH chr8 + 97719048 97719189 1.45E−05 0.00182274 NC
MAP4K4 chr2 + 101860824 101860986 0.00207288 0.04372388 UP
MAP4K4 chr2 + 101863820 101864051 2.52E−10 6.73E−07 DN
BCAS1 chr20 − 53957431 53957497 0.00014617 0.00862437 UP
TRAPPC12 chr2 + 3477694 3477795 0.00185734 0.04087953 UP
PHYHIP chr8 − 22228787 22228909 1.61E−05 0.00196115 UP
SYNE1 chr6 − 152130719 152130778 0.00033978 0.01429316 UP
KCNC3 chr19 − 50316032 50316091 0.00011194 0.0070884 UP
ACAA1 chr3 − 38126161 38126341 0.00057348 0.01939066 DN
RNF146 chr6 + 127285207 127285348 0.00027653 0.01288046 UP
GSTO1 chr10 + 104262978 104263077 2.59E−07 0.00010575 DN
ARHGAP12 chr10 − 31839636 31839711 0.00092024 0.02613029 UP
AP1G2 chr14 − 23565815 23565892 4.26E−05 0.00368385 DN
PHLDB1 chr11 + 118655859 118655892 9.45E−05 0.00623718 UP
SH3YL1 chr2 − 224863 224920 0.00048615 0.01763532 UP
NRCAM chr7 − 108237751 108237769 0.00029057 0.01323689 UP
ASPH chr8 − 61646749 61646878 0.00104222 0.02827661 UP
ASPDH chr19 − 50512926 50513011 0.00108324 0.02890907 DN
ZIM2 chr19 − 56826387 56826463 0.00058246 0.01955921 UP
CHL1 chr3 + 342983 343031 0.0006118 0.02015719 DN
COL16A1 chr1 − 31679803 31679851 0.00221949 0.04572039 DN
PRKACB chr1 + 84175798 84175807 1.79E−05 0.00209292 UP
GANAB chr11 − 62634309 62634375 2.51E−06 0.00055786 DN
RHBDD2 chr7 + 75881364 75881486 0.00130743 0.03270973 UP
TJP1 chr15 − 29719776 29720016 3.72E−06 0.00078017 DN
KIF3A chr5 − 132708906 132708974 9.44E−06 0.00137048 DN
GOLIM4 chr3 − 168040785 168040869 0.00117628 0.0306136 UP
CBWD1 chr9 − 177722 177820 0.00042182 0.01620172 DN
ITSN2 chr2 − 24284762 24284843 7.09E−06 0.00115732 UP
DAP3 chr1 + 155729041 155729122 0.00082594 0.02426863 UP
CCDC136 chr7 + 128806236 128806395 0.00165475 0.03789665 DN
CLASP2 chr3 − 33577201 33577264 0.00090364 0.02587886 DN
NCOA1 chr2 + 24768078 24768135 2.16E−05 0.00242146 UP
GNAS chr20 + 58898940 58898985 0.00164511 0.03776438 NC
RBFOX1 chr16 + 7693314 7693367 0.00099681 0.02736915 UP
CEP290 chr12 − 88054339 88054413 9.27E−05 0.00618541 UP
PUF60 chr8 − 143820665 143820716 6.52E−05 0.00489236 UP
SLC25A23 chr19 − 6453980 6454088 0.00112685 0.02964206 NC
MEG3 chr14 + 100834631 100834751 6.17E−05 0.0047638 NC
MEG3 chr14 + 100835738 100835879 0.00141988 0.03434764 NC
FN1 chr2 − 215372108 215372300 3.99E−06 0.00081892 UP
FN1 chr2 − 215372108 215372375 7.23E−07 0.00020244 UP
DTNA chr18 + 34866110 34866131 0.00228755 0.04652658 DN
GPM6A chr4 − 175812190 175812249 1.24E−08 1.02E−05 UP
OLA1 chr2 − 174246714 174246815 0.00057014 0.01936578 DN
YWHAZ chr8 − 100951928 100952125 6.18E−05 0.0047638 UP
RNASE1 chr14 − 20802248 20802319 9.31E−05 0.00618541 DN
RNASE1 chr14 − 20802248 20802331 6.42E−05 0.00487467 DN
CALU chr7 + 128754528 128754722 0.00187284 0.04109756 UP
ALG8 chr11 − 78102873 78102948 3.69E−07 0.00012922 UP
TABLE 23
CARRIER_VS_TD_MXE
geneSymbol chr strand 1stExonStart_0base 1stExonEnd 2ndExonStart_0base 2ndExonEnd PValue FDR type
FYN chr6 − 111699514 111699670 111700103 111700268 0.0001885 0.0096127 UP
PIBF1 chr13 + 72965273 72965404 72973590 72973675 0.00116618 0.02927732 DN
TBC1D5 chr3 − 17238162 17238419 17258505 17258591 0.00019191 0.0096127 UP
TNRC6A chr16 + 24758338 24758360 24776932 24777358 0.0001441 0.00827948 UP
SEZ6L chr22 + 26365371 26365566 26375574 26375689 1.72E−05 0.00172028 DN
SEZ6L chr22 + 26365371 26365566 26375577 26375689 1.05E−05 0.0011766 DN
ZMAT4 chr8 − 40581164 40581261 40674703 40674931 0.00022382 0.01053576 UP
MOBP chr3 + 39480039 39480123 39499466 39499532 0.0007262 0.02234068 NC
PDXDC1 chr16 + 15001775 15001856 15004186 15004333 0.0011669 0.02927732 UP
TPM3 chr1 − 154170648 154170711 154172028 154172104 0.00213151 0.04360117 DN
ANKRD24 chr19 + 4199874 4200005 4200082 4200171 0.00012217 0.00723224 DN
WIPF2 chr17 + 40262524 40262641 40264489 40265146 0.00096758 0.02662204 UP
ATRNL1 chr10 + 115315517 115315736 115334281 115334419 3.92E−05 0.00312596 UP
FXYD7 chr19 + 35151253 35151328 35151439 35151473 0.00212545 0.04360117 DN
TSSC1 chr2 − 3257298 3257455 3338016 3338149 2.65E−05 0.00229997 DN
RP11- chr18 + 9124873 9124983 9126830 9126907 2.08E−08 9.02E−06 DN
21J18.1
PAQR6 chr1 − 156245534 156245661 156245781 156245987 0.00210179 0.04360117 NC
MGEA5 chr10 − 101800241 101800400 101803734 101804019 0.0005927 0.01945942 DN
ANK3 chr10 − 60200128 60200227 60203001 60203100 0.00116899 0.02927732 DN
PITPNC1 chr17 + 67532801 67532950 67552256 67552345 0.00090702 0.02552935 UP
MAPT chr17 + 45962320 45962470 45971858 45971945 0.0003531 0.01385376 UP
VCAN chr5 + 83519348 83522309 83537006 83542268 8.51E−05 0.00563641 DN
DAB2IP chr9 + 121759884 121760439 121763504 121763649 0.00077255 0.02321801 DN
PRKAG2 chr7 − 151595344 151595454 151632068 151632138 0.0018563 0.04029196 UP
SETD4 chr21 − 36048307 36048396 36053582 36053620 0.00204734 0.04330727 UP
SMARCA4 chr19 + 11007901 11008023 11010380 11010531 0.00043714 0.01611235 UP
BAZ2B chr2 − 159448241 159448403 159453612 159453801 0.00088355 0.02552935 DN
BAZ2B chr2 − 159448241 159448409 159453612 159453801 0.00207445 0.04334168 DN
RBFA chr18 + 80038504 80038617 80042134 80042219 2.78E−05 0.00236311 UP
LUC7L chr16 − 220648 220747 227241 227336 0.00146784 0.03454721 DN
AIF1 chr6 + 31615669 31615736 31616103 31616145 0.00177591 0.0396485 DN
PDE2A chr11 − 72631077 72631139 72642253 72642326 0.00250474 0.0491759 DN
CAMK2G chr10 − 73825278 73825347 73828088 73828121 0.00035499 0.01385376 DN
CAMK2G chr10 − 73825278 73825347 73828088 73828121 0.00047163 0.01675142 DN
CCDC7 chr10 + 32567669 32567891 32583033 32583307 0.00205141 0.04330727 UP
PMS1 chr2 + 189863742 189863974 189867798 189867929 0.00166957 0.037989 UP
PMS1 chr2 + 189863742 189864228 189867798 189867929 0.00115616 0.02927732 UP
ADCK4 chr19 − 40705324 40705447 40710058 40710136 0.00139712 0.03328376 UP
CRELD2 chr22 + 49923233 49923317 49924359 49924455 0.00031569 0.01326252 DN
ARID4A chr14 + 58360900 58361042 58364169 58365300 6.83E−05 0.00503336 UP
MTDH chr8 + 97699753 97699852 97706625 97706750 0.00032343 0.01330165 DN
MAP4K4 chr2 + 101860824 101860986 101863820 101864051 4.74E−14 1.85E−10 UP
ACTR1B chr2 − 97660570 97660646 97661881 97661946 0.000288 0.01250239 DN
BCAS3 chr17 + 61078332 61078529 61084466 61084564 9.91E−05 0.00604969 DN
GTF2A2 chr15 − 59650668 59650773 59652205 59652326 0.00074271 0.02266993 UP
C11orf80 chr11 + 66788159 66788269 66796280 66796364 8.12E−06 0.00103464 UP
ZNF106 chr15 − 42442072 42442414 42444201 42444262 0.00031208 0.01325331 UP
ZNF106 chr15 − 42448071 42448705 42466052 42466114 0.00107974 0.02850378 DN
SESN1 chr6 − 108990644 108990835 108992786 108992899 1.37E−08 8.90E−06 UP
PHYHD1 chr9 + 128940368 128940497 128940598 128940715 0.00056706 0.01893578 DN
GRID1 chr10 − 85869009 85869180 85916185 85916239 0.00253 0.0494236 UP
MAP9 chr4 − 155355715 155355884 155357448 155357519 0.00091464 0.02552935 DN
NRCAM chr7 − 108166920 108167073 108168276 108168402 0.00206172 0.04330727 UP
ASPDH chr19 − 50512135 50512290 50512926 50513011 0.00042917 0.01596935 UP
VIPR1 chr3 + 42532241 42532333 42534974 42535104 8.20E−05 0.00562087 DN
PLEKHA6 chr1 − 204250545 204250614 204251530 204251611 9.64E−05 0.00597536 DN
ADAL chr15 + 43334944 43335170 43335695 43335826 2.97E−06 0.00048297 UP
C11orf74 chr11 + 36636050 36636117 36648015 36648155 0.00195189 0.04167242 DN
SYMPK chr19 − 45838460 45838615 45842249 45842489 0.00033373 0.01358205 UP
RANGAP1 chr22 − 41274599 41274727 41280932 41281082 0.00168609 0.03807833 DN
PON2 chr7 − 95412311 95412477 95416241 95416297 0.00249155 0.04916413 UP
ITSN2 chr2 − 24275712 24275849 24286211 24286351 0.00018966 0.0096127 DN
SNW1 chr14 − 77720710 77720828 77723180 77723277 0.00015567 0.00856649 UP
SPG11 chr15 − 44585635 44585850 44589251 44589414 0.00149353 0.03479665 UP
RGL1 chr1 + 183806374 183806485 183847565 183847774 0.00015307 0.00854367 UP
CCDC136 chr7 + 128807359 128807545 128817757 128817864 0.0019377 0.0415967 NC
HACE1 chr6 − 104833041 104833173 104843222 104843298 0.00239699 0.04778084 UP
SLC1A3 chr5 + 36608328 36608604 36629449 36629587 0.00182552 0.04006917 DN
BRWD1 chr21 − 39238478 39238573 39247700 39247832 0.00104763 0.02803498 DN
PSMB1 chr6 − 170537233 170537340 170543600 170543730 0.00042318 0.01589761 DN
CUX2 chr12 + 111291417 111291552 111293445 111293569 0.00020506 0.01001475 DN
VPS26A chr10 + 69166041 69166110 69168488 69168631 2.22E−05 0.00201507 DN
EGFL7 chr9 + 136664691 136664785 136668240 136668362 0.00049378 0.01738029 DN
ADCK2 chr7 + 140681041 140681137 140686989 140687241 0.00035813 0.01385376 DN
ZNF415 chr19 − 53115209 53115307 53115703 53115811 0.00104564 0.02803498 DN
ANAPC16 chr10 + 72223887 72224056 72230365 72230440 0.00044252 0.01615836 UP
CCM2 chr7 + 45038252 45038426 45072725 45072783 0.00064624 0.02046533 DN
CCM2 chr7 + 45069825 45069961 45072725 45072783 0.00072127 0.02234068 NC
ARL3 chr10 − 102699372 102699489 102705345 102705489 0.00103662 0.02803498 UP
ARCN1 chr11 + 118593589 118593698 118597706 118597911 2.49E−06 0.00046342 DN
CALU chr7 + 128754261 128754455 128754528 128754722 5.21E−05 0.00407347 DN
TABLE 24
CARRIER_VS_TD_DE
gene_symbol FXS_patient_vs_healthy_type
ADGRL4 DN
APOLD1 DN
BLOC1S5-TXNDC5 UP
C10orf10 DN
CD93 DN
ELOVL7 DN
F8A3 DN
FCGR3A DN
FER1L6 UP
ITGA6 DN
KIF25 UP
MIR143HG UP
NUTM2E UP
OR7D2 DN
PECAM1 DN
POC1B-GALNT4 UP
RP11-17M24.3 UP
RP11-73M18.2 DN
RP11-986E7.7 DN
RPL17-C18orf32 DN
S100A9 DN
SST UP
TBC1D3L UP
TVP23C-CDRT4 DN
VSIG4 DN
XXbac-BPG246D15.9 UP
Legends for Tables 3-10 and 16-24:
-
- SE: Skipped exon
- MXE: Mutually exclusive exons
- A3SS: Alternative 3′ splice site
- A5SS: Alternative 5′ splice site
- ENSEMBL Gene ID
- Chr: chromosome
- Strand: Strand
- exonStart_0base: start position of the skipped exon
- exonEnd: end position of the skipped exon
- 1 stExonStart_0base: start position of the 1st exon in MXE
- 1 stExonEnd: end position of the 1st exon in MXE
- 2ndExonStart_0base: start position of the 2nd exon in MXE
- 2nd ExonEnd: end position of the 2nd exon in MXE
- longExonStart_0base: start position of the long exon in A3SS or A5SS
- longExonEnd: end position of the long exon in A3SS or A5SS
- shortES: start position of the short exon in A3SS or A5SS
- shortEE: end position of the short exon in A3SS or A5SS
- flankingES: start position of the closest flanking exon in A3SS or A5SS
- flankingEE: end position of the closest flanking exon in A3SS or A5SS
- upstreamES: start position of the closest upstream exon
- upstreamEE: end position of the closest upstream exon
- downstreamES: start position of the closest downstream exon
- downstreamEE: end position of the closest downstream exon
- IncLevelDifference: IncLevelDifference: average (IncLevel FXS)—average (IncLevel Control)
- Type: Up, significantly increased splicing in FXS; DN, significantly increased splicing in Control; NC, no change.
- P-Value: Significance of splicing difference between two groups.
- FDR: False Discovery Rate calculated from p-value.
EMBODIMENTS 1. A method of diagnosing a subject as having, or having a propensity to develop, fragile X syndrome (FXS), comprising assaying at least one RNA biomarker in a biological sample from the subject, wherein the level and/or splicing of the at least one RNA biomarker in the biological sample is indicative of the subject as having, or having a propensity to develop, FXS, and wherein the biological sample is a non-neural biological sample.
2. A method of prognosing fragile X syndrome (FXS) in a subject, comprising assaying at least one RNA biomarker in a biological sample from the subject, wherein the level and/or splicing of the at least one RNA biomarker in the biological sample is indicative of the subject as having a propensity to have a poorer prognosis of FXS, and wherein the biological sample is a non-neural biological sample.
3. A method of predicting a treatment outcome of fragile X syndrome (FXS) in a subject, comprising assaying at least one RNA biomarker in a biological sample from the subject, wherein the level and/or splicing of the at least one RNA biomarker in the biological sample is indicative of the subject as having a propensity to have a poorer treatment outcome, and wherein the biological sample is a non-neural biological sample.
4. A method of stratifying a set of subjects having fragile X syndrome (FXS), comprising assaying at least one RNA biomarker in a biological sample from the subject, and stratifying the set of subjects for treatment based on the level or splicing of the at least one RNA biomarker in the biological sample, wherein the biological sample is a non-neural biological sample.
5. The method of any one of Embodiments 1-4, wherein the biological sample is a bodily fluid sample, a hair sample, buccal swab sample or a skin sample.
6. The method of Embodiment 5, wherein the bodily fluid sample comprises blood, saliva, tears, urine or semen.
7. The method of Embodiment 5, wherein the bodily fluid sample comprises white blood cells.
8. The method of any one of Embodiments 1-7, wherein the at least one RNA biomarker is selected from the group consisting of AGAP1, RAB25, FAM3B, XKR3, MAP3K15, LEP, RP11-706O15.3, GCOM1, CXCL6, RGL3, NECAB2, TGM3, LRRC6, MAB21L3, RP11-36B15.1, AC091878.1, RP11-154H23.3, NOV, AC093495.4, RP11-455F5.6, RGPD2, COL9A3, CLEC18A, RP11-256L6.2, LINC01127, SLC38A11, EFCAB12, LA16c-380H5.5, CXCL1, RP11-1334A24.5, AC100793.2, ANKDD1A, AVIL, RP11-44F14.8, RP11-290F20.1, AC116366.5, EPHB4, ST6GALNAC3, PANX2, CREB5, KIAA0319, HECW2, ADCY4, LINC000173, RP11-59D5_B.2, RP11-274B18.2, RP11-213H15.3, CORO7-PAM16, HAL, DPEP3, AC002467.7, MGAM, PNMA8A, FMR1, S100B, RP11-885N19.6, RP11-545I5.3, AC091814.2, KLRC2, L1TD1, PGBD5, MXRA7, CROCC2, SEMA5A, PLA2G4C, RP11-1008C21.1, TANC1, C4orf50, NUAK1, AC104809.4, RGS17, KCNS1, DRAXIN, B3GAT1, ARHGEF28, KIF19, APOL4, GZMH, GAS1, SCD5, GLB1L2, IGHA1, KNDC1, RP11-383H13.1, FGFR2, TFCP2L1, PDGFRB, LAG3, GPR153, PODN, CKB, CERCAM, ZNF365, JUP, TRNP1, JAKMIP1, CPXM1, SLC1A7, LGR6, FCRL6, MORN4, TUBB2A, PRSS23, BFSP1, NCALD, ZNF573, PAK1, MIR4435-2HG, CD8B, PDGFC, TRAPPC2L, AC006504.5, ZNF512, FAM228B, NEIL2, FAM78A, FYB1, RNF216P1, ZCWPW1, DTX2, ATP5MD, MX2, LYRM1, GUF1, DPH7, NSFL1C, MTMR1, GTPBP10, RGS3, DRAM2, RHOH, LAIR2, GBP3, GTF2H1, XPNPEP3, ZNF888, TBC1D5, AC060780.1, SDHAP2, KMT2A, SH3BP2, CSNK1G2, NSUN5P1, LINC01128, RNF19A, SNHG8, TOP1MT, AL135818.1, CR1, CRIM1, NAP1L1, AC004593.2, SEC61A2, PCNX2, TPT1-AS1, HLA-A, LUCAT1, PTPN2, SEC31B, POLR2J3, POLR2J4, CAST, POLR2J4, NUMBL, PRMT7, ATF7IP2, TIMM23B-AGAP6, ADGRE2, GTF2H2B, MICA, SLC29A2, ZBTB10, NLGN3, METTL25, ADAM15, SSH1, SIRPB1, PARP2, PACRGL, ENTPD1-AS1, FUZ, SDR39U1, EPOR, ZSCAN26, SNHG17, GPS2, NECAP1, MRPLI1, DNAJC19, ANKZF1, C1orf162, PIGT, SLC25A37, AP1G1, CIC, ITGB7, ATG16L2, BECN1, ARHGEF40, BANP, PIGA, RAD52, IRF3, CEP78, SPINT1, TMEM156, NT5C3B, PLD2, ANKRD12, CASP8, PACS2, HLA-DMA, DHPS, PDCD6, SNX5, MPPE1, AC016394.2, DPM1, E2F5, PTPN7, MTFP1, TOR1AIP1, POT1, JOSD2, NLRX1, FDXR, ZDHHC16, ALKBH4, RPS9, ZNF302, TENT4B, TKT, CARD8, RBM26, WSB1, DDX60L, ATP11A, SRGAP2, CEACAM21, COX18, WDR47, PATZ1, POLM, CC2D1B, CLK4, MIB2, PHF1, KANSL1, TCF3, and combinations thereof.
9. The method of Embodiment 8, wherein the at least one RNA biomarker has an increased expression in the biological sample, relative to a control sample.
10. The method of Embodiment 9, wherein the expression of at least one RNA biomarker has a log 2 fold increase of ≥0.80 in the biological sample, relative to a control sample, optionally, wherein the log 2 fold increase is ≥0.95.
11. The method of Embodiment 9 or 10, wherein the at least one RNA biomarker is selected from the group consisting of AGAP1, RAB25, FAM3B, XKR3, MAP3K15, LEP, RP11-706O15.3, GCOM1, CXCL6, RGL3, NECAB2, TGM3, LRRC6, MAB21L3, RP11-36B15.1, AC091878.1, RP11-154H23.3, NOV, AC093495.4, RP11-455F5.6, RGPD2, COL9A3, CLEC18A, RP11-256L6.2, LINC01127, SLC38A11, EFCAB12, LA16c-380H5.5, CXCL1, RP11-1334A24.5, AC100793.2, ANKDD1A, AVIL, RP11-44F14.8, RP11-290F20.1, AC116366.5, EPHB4, ST6GALNAC3, PANX2, CREB5, KIAA0319, HECW2, ADCY4, LINC00173, RP11-59D5_B.2, RP11-274B18.2, RP11-213H15.3, CORO7-PAM16, HAL, DPEP3, AC002467.7, MGAM, PNMA8A, and combinations thereof.
12. The method of Embodiment 8, wherein the at least one RNA biomarker has a reduced expression in the biological sample, relative to a control sample.
13. The method of Embodiment 12, wherein the expression of the at least one RNA biomarker has a log 2 fold reduction of ≥1.00 in the biological sample, relative to a control sample, optionally, the log 2 fold reduction is ≥1.16.
14. The method of Embodiment 12 or 13, wherein the at least one RNA biomarker is selected from the group consisting of FMR1, S100B, RP11-885N19.6, RP11-545I5.3, AC091814.2, KLRC2, L1TD1, PGBD5, MXRA7, CROCC2, SEMA5A, PLA2G4C, RP11-1008C21.1, TANC1, C4orf50, NUAK1, AC104809.4, RGS17, KCNS1, DR AXIN, B3GAT1, ARHGEF28, KIF19, APOL4, GZMH, GAS1, SCD5, GLB1L2, IGHA1, KNDC1, RP11-383H13.1, FGFR2, TFCP2L1, PDGFRB, LAG3, GPR153, PODN, CKB, CERCAM, ZNF365, JUP, TRNP1, JAKMIP1, CPXM1, SLC1A7, LGR6, FCRL6, MORN4, TUBB2A, PRSS23, BFSP1, and combinations thereof.
15. The method of Embodiment 8, wherein the at least one RNA biomarker has a reduced exon skipping in the biological sample, relative to a control sample.
16. The method of Embodiment 15, wherein the reduction is ≥13.0%, optionally, the reduction is ≥16.0%.
17. The method of Embodiment 15 or 16, wherein the at least one RNA biomarker is selected from the group consisting of NCALD, ZNF573, PAK1, MIR4435-2HG, CD8B, PDGFC, TRAPPC2L, AC006504.5, ZNF512, FAM228B, NEIL2, FAM78A, FYB1, RNF216P1, ZCWPW1, DTX2, ATP5MD, MX2, LYRM1, GUF1, DPH7, NSFL1C, MTMR1, GTPBP10, RGS3, and combinations thereof.
18. The method of Embodiment 17, wherein the skipped exon is selected from the group consisting of the skipped exons listed in Table 3.
19. The method of Embodiment 8, wherein the at least one RNA biomarker has an increased exon skipping in the biological sample, relative to a control sample.
20. The method of Embodiment 19, wherein the increase is ≥13.0%, optionally, wherein the increase is ≥17.0%.
21. The method of Embodiment 19 or 20, wherein the at least one RNA biomarker is selected from the group consisting of NCALD, DRAM2, RHOH, LAIR2, GBP3, GTF2H1, XPNPEP3, ZNF888, TBC1D5, AC060780.1, SDHAP2, KMT2A, SH3BP2, CSNK1G2, ATP5MD, NSUN5P1, LINC01128, RNF19A, SNHG8, TOP1MT, AL135818.1, and combinations thereof.
22. The method of Embodiment 21, wherein the skipped exon is selected from the group consisting of the skipped exons listed in Table 4.
23. The method of Embodiment 8, wherein the at least one RNA biomarker has a reduced mutually exclusive exon switching in the biological sample, relative to a control sample.
24. The method of Embodiment 23, wherein the reduction is ≥10.0%, optionally, the reduction is ≥13.0%.
25. The method of Embodiment 23 or 24, wherein the at least one RNA biomarker is selected from the group consisting of CR1, CRIM1, ZCWPW1, NAPIL1, TBC1D5, MIR4435-2HG, AC004593.2, GBP3, SEC61A2, PCNX2, TPT1-AS1, HLA-A, LUCAT1, PTPN2, SEC31B, POLR2J3, POLR2J4, CAST, NUMBL, PRMT7, ATF7IP2, TIMM23B-AGAP6, and combinations thereof.
26. The method of Embodiment 25, wherein the mutually exclusive exon is selected from the group consisting of the mutually exclusive exons listed in Table 5.
27. The method of Embodiment 8, wherein the at least one RNA biomarker has an increased mutually exclusive exon switching in the biological sample, relative to a control sample.
28. The method of Embodiment 23, wherein the increase is ≥12.0%, optionally, the increase is ≥15.0%.
29. The method of Embodiment 27 or 28, wherein the at least one RNA biomarker is selected from the group consisting of HLA-A, ADGRE2, PAK1, TBC1D5, GTF2H2B, MICA, SLC29A2, ZBTB10, NLGN3, CAST, METTL25, ADAM15, LUCAT1, SSH1, SIRPB1, GBP3, and combinations thereof.
30. The method of Embodiment 29, wherein the mutually exclusive exon is selected from the group consisting of the mutually exclusive exons listed in Table 6.
31. The method of Embodiment 8, wherein the at least one RNA biomarker has a reduced alternative 5′ splicing in the biological sample, relative to a control sample.
32. The method of Embodiment 31, wherein the reduction is ≥4.5%, optionally, the reduction is ≥5.0%.
33. The method of Embodiment 31 or 32, wherein the at least one RNA biomarker is selected from the group consisting of PARP2, PACRGL, ENTPD1-AS1, NEIL2, FUZ, SDR39U, ADAM15, EPOR, ZSCAN26, SNHG17, GPS2, NECAP1, MRPLI1, DNAJC9, ANKZF1, C1orf162, PIGT, SLC25A37, AP1G1, CIC, ITGB7, ATG16L2, BECN1, ARHGEF40, and combinations thereof.
34. The method of Embodiment 33, wherein the alternative 5′ splicing site is selected from the alternative 5′ splicing sites listed in Table 7.
35. The method of Embodiment 8, wherein the at least one RNA biomarker has an increased alternative 5′ splicing in the biological sample, relative to a control sample.
36. The method of Embodiment 35, wherein the increase is 4.5%, optionally, the increase is ≥5.5%.
37. The method of Embodiment 35 or 36, wherein the at least one RNA biomarker is selected from the group consisting of BANP, PIGA, SNHG8, RAD52, IRF3, CEP78, SPINT1, TMEM156, NT5C3B, PLD2, HLA-A, ANKRD12, CASP8, PACS2, HLA-DMA, DHPS, PDCD6, and combinations thereof.
38. The method of Embodiment 37, wherein the alternative 5′ splicing site is selected from the alternative 5′ splicing sites listed in Table 8.
39. The method of Embodiment 8, wherein the at least one RNA biomarker has a reduced alternative 3′ splicing in the biological sample, relative to a control sample.
40. The method of Embodiment 39, wherein the reduction is 6.5%, optionally, the reduction is ≥7.5%.
41. The method of Embodiment 39 or 40, wherein the at least one RNA biomarker is selected from the group consisting of SNX5, POLR2J3, MPPE1, AC016394.2, DPM1, E2F5, PTPN7, MTFP1, TOR1AIP1, POT1, JOSD2, NLRX1, FDXR, ZDHHC16, ALKBH4, RPS9, ZNF302, TENT4B, ADGRE2, TKT, CARD8, RBM26, WSB1, and combinations thereof.
42. The method of Embodiment 41, wherein the alternative 3′ splicing site is selected from the alternative 3′ splicing sites listed in Table 9.
43. The method of Embodiment 8, wherein the at least one RNA biomarker has an increased alternative 3′ splicing in the biological sample, relative to a control sample.
44. The method of Embodiment 43, wherein the increase is ≥4.5%, optionally, the increase is ≥5.0%.
45. The method of Embodiment 43 or 44, wherein the at least one RNA biomarker is selected from the group consisting of DDX60L, ATP11A, SRGAP2, CEACAM21, COX18, WDR47, PATZ1, POLM, CC2DIB, CLK4, MIB2, PHF1, KANSL1, TCF3, and combinations thereof.
46. The method of Embodiment 45, wherein the alternative 3′ splicing site is selected from the alternative 3′ splicing sites listed in Table 10.
47. The method of any one of Embodiments 1-46, comprising assaying at least 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, 40 or 45 RNA markers in the biological sample from the subject.
48. The method of any one of Embodiments 1-47, wherein assaying the at least one RNA biomarker comprises performing quantitative RT-PCR, microarray, cDNA sequencing (RNA-Seq), or a combination thereof.
49. The method of any one of Embodiments 1-48, wherein the subject is a human male.
50. The method of any one of Embodiments 1-48, wherein the subject is a human female.
51. The method of any one of Embodiments 1-50, wherein the at least one RNA biomarker comprises fragile X mental retardation 1 (FMR1).
52. The method of Embodiment 51, wherein isoform 12 of FMR1 RNA has an increased expression in the biological sample, relative to a control sample.
53. The method of any one of Embodiments 1-52, wherein the control sample is from an age-matched sample from a typically developing subject.
54. The method of any one of Embodiments 1-52, wherein the control sample is a theoretical value calculated from the general population.
55. The method of any one of Embodiments 1-52, wherein the control sample is a baseline sample of the subject.
56. The method of any one of Embodiments 1-55, further comprising treating the subject.
57. A system, comprising one or more polynucleotide probes and/or one or more polynucleotide primers configured to detect, in a biological sample, the level and/or splicing of the at least one RNA biomarker associated with fragile X syndrome (FXS).
58. The system of Embodiment 57, wherein the at least one RNA biomarker is selected from the group consisting of AGAP1, RAB25, FAM3B, XKR3, MAP3K15, LEP, RP11-706O15.3, GCOM1, CXCL6, RGL3, NECAB2, TGM3, LRRC6, MAB21L3, RP11-36B15.1, AC091878.1, RP11-154H23.3, NOV, AC093495.4, RP11-455F5.6, RGPD2, COL9A3, CLEC18A, RP11-256L6.2, LINC01127, SLC38A11, EFCAB12, LA16c-380H5.5, CXCL1, RP11-1334A24.5, AC100793.2, ANKDD1A, AVIL, RP11-44F14.8, RP11-290F20.1, AC116366.5, EPHB4, ST6GALNAC3, PANX2, CREB5, KIAA0319, HECW2, ADCY4, LINC00173, RP11-59D5_B.2, RP11-274B18.2, RP11-213H15.3, CORO7-PAM16, HAL, DPEP3, AC002467.7, MGAM, PNMA8A, FMR1, S100B, RP11-885N19.6, RP11-545I5.3, AC091814.2, KLRC2, L1TD1, PGBD5, MXRA7, CROCC2, SEMA5A, PLA2G4C, RP11-1008C21.1, TANC1, C4orf50, NUAK1, AC104809.4, RGS17, KCNS1, DRAXIN, B3GAT1, ARHGEF28, KIF19, APOL4, GZMH, GAS1, SCD5, GLB1L2, IGHA1, KNDC1, RP11-383H13.1, FGFR2, TFCP2L1, PDGFRB, LAG3, GPR153, PODN, CKB, CERCAM, ZNF365, JUP, TRNP1, JAKMIP1, CPXM1, SLC1A7, LGR6, FCRL6, MORN4, TUBB2A, PRSS23, BFSP1, NCALD, ZNF573, PAK1, MIR4435-2HG, CD8B, PDGFC, TRAPPC2L, AC006504.5, ZNF512, FAM228B, NEIL2, FAM78A, FYB1, RNF216P1, ZCWPW1, DTX2, ATP5MD, MX2, LYRM1, GUF1, DPH7, NSFL1C, MTMR1, GTPBP10, RGS3, DRAM2, RHOH, LAIR2, GBP3, GTF2H1, XPNPEP3, ZNF888, TBC1D5, AC060780.1, SDHAP2, KMT2A, SH3BP2, CSNK1G2, NSUN5P1, LINC01128, RNF19A, SNHG8, TOP1MT, AL135818.1, CR1, CRIM1, NAP1L1, AC004593.2, SEC61A2, PCNX2, TPT1-AS1, HLA-A, LUCAT1, PTPN2, SEC31B, POLR2J3, POLR2J4, CAST, POLR2J4, NUMBL, PRMT7, ATF7IP2, TIMM23B-AGAP6, ADGRE2, GTF2H2B, MICA, SLC29A2, ZBTB10, NLGN3, METTL25, ADAM15, SSH1, SIRPB1, PARP2, PACRGL, ENTPD1-AS1, FUZ, SDR39U1, EPOR, ZSCAN26, SNHG17, GPS2, NECAP1, MRPL11, DNAJC19, ANKZF1, C1orf162, PIGT, SLC25A37, AP1G1, CIC, ITGB7, ATG16L2, BECN1, ARHGEF40, BANP, PIGA, RAD52, IRF3, CEP78, SPINT1, TMEM156, NT5C3B, PLD2, ANKRD12, CASP8, PACS2, HLA-DMA, DHPS, PDCD6, SNX5, MPPE1, AC016394.2, DPM1, E2F5, PTPN7, MTFP1, TOR1AIP1, POT1, JOSD2, NLRX1, FDXR, ZDHHC16, ALKBH4, RPS9, ZNF302, TENT4B, TKT, CARD8, RBM26, WSB1, DDX60L, ATP11A, SRGAP2, CEACAM21, COX18, WDR47, PATZ1, POLM, CC2D1B, CLK4, MIB2, PHF1, KANSL1, TCF3, and combinations thereof.
59. The system of Embodiment 58, wherein one or more polynucleotide probes are immobilized on a solid substrate.
60. The system of Embodiment 59, wherein the system is a microarray.
61. A method of stratifying a population of subjects having, or having a propensity to develop, fragile X syndrome (FXS), comprising assaying biological samples from the subjects for the presence of fragile X mental retardation 1 (FMR1) RNA isoform 12.
62. A method for assessing the efficacy of a drug for treatment of fragile X syndrome (FXS), comprising stratifying a population of subjects by the method of Embodiment 61 to create a stratified population comprising a subpopulation who has the FMR1 RNA isoform 12 and a subpopulation who does not have the FMR1 RNA isoform 12, and administering the drug to the subpopulation who has FMR1 RNA isoform 12, or to both subpopulations.
63. A method of stratifying a set of subjects having fragile X syndrome (FXS), comprising assaying fragile X mental retardation 1 (FMR1) RNA in a biological sample from the subject, and stratifying the set of subjects for treatment based on the presence and/or level of the FMR1 RNA isoform 12 in the biological sample.
64. The method of any one of Embodiments 61-63, wherein the biological sample is a non-neural biological sample.
65. The method of Embodiment 1, further comprising treating the subject if the subject is diagnosed to have, or has a propensity to develop, fragile X syndrome (FXS).
66. The method of any one of Embodiments 1-56, wherein the at least one RNA biomarker is selected from the group consisting of ANAPC1P2, FAM3B, HMGB1P5, CYP4F22, RHOC, AGAP1, CFAP70, KNDC1, PRR5L, ZNF365, DUSP5, ARHGAP24, EPOP, MXRA7, TOMM5, TRBV2, NKG7, CLEC5A, TKTL1, RAB25, COL13A1, RBM11, AC008764.4, CKB, GNGT2, LAMC3, NEFL, ZNF154, C12orf75, MSC-AS1, RPL39L, PPFIBP1, ACOT7, CDKN1C, CKS1B, LINC00174, PALM, CABP4, EFNA5, LYPD2, DRAXIN, B3GAT1, TPST2, CROCC2, FCRL6, AC026369.3, C19orf12, S100B, GAS1, JAKMIP1, LINC02345, GPR153, S1PR5, MIR3150BHG, and combinations thereof.
67. The method of any one of Embodiments 1-56, wherein the skipped exon is selected from the group consisting of PARP6, NCALD, PACRGL, TCF7, ADAM15, LAIR2, XPNPEP3, ADAM15, POLR2J3, POLR2J3, LINC00937, WARS1, ADAM15, ADAM15, AL135818.1, AC092070.2, TRPT1, DST, WARS1, MIR4435-2HG, LRRFIP1, ADCY10P1, RNF19A, DRAM2, TRPV2, CAST, C11orf80, ZNF266, HMOX2, JPX, ZNF266, DPM1, FRG1, FRG1, COPS3, METTL8, FCRLA, WARS1, WARS1, PMS2CL, MUC20-OT1, ZNF273, NQO2, AC141586.1, PNPO, BFAR, GBAP1, RAB18, GPS1, TAF5, HMOX2, PACRGL, IZUMO4, ANKS3, SEPTIN2, YY1AP1, OFD1, AC012184.3, SEPTIN2, LAIR2, SEPTIN2, LDAH, CDC42BPG, ZNF273, VMP1, ATP6AP1L, COMMD2, PPRC1, RHBDF2, ZNF56, SRSF4, ZNF529-AS1, TNK2, ANKS3, SUCO, TBC1D19, WARS1, ITGB7, CYB5RL, WARS1, IFI44L, TGIF1, ZBTB25, FKRP, NSUN5P1, ADAM15, PRKCQ-AS1, TRPT1, NCAPG2, IP6K2, ALS2CL, NFS1, LINC00174, CYRIB, CDC27, ZNF202, GOLGA2P5, ZNF85, FBXW8, COA8, NSRP1, KLRC4-KLRK1, OFD1, FKRP, BCLAF3, SRPK2, WARS1, HPCAL1, RXYLT1, CARMIL1, RAD51C, HEATR6, CROCC, AL732372.2, DTNB, PLPP1, CTNS, COP1, NEK3, POLA1, LSM14B, CCDC18-AS1, LYPLAL1-DT, SLC25A43, BRAF, STX3, PPFIA1, UBR2, SRP14-AS1, ZBTB7B, BCLAF3, SF11, FKRP, STAG3L3, IMMP1L, PNPO, BBS2, PIGT, PAAF1, NQO2, NT5DC2, PRKCQ-AS1, OSBPL5, MAPKAPK5, ITGAE, PCBP1-AS1, FAM229B, ZSCAN25, OBSCN, HDAC10, ACAD10, JPX, NUBP2, FRG1BP, PDPR, RAB3IP, HEATR3, LSM14B, POGLUT3, TPP2, TRPM7, NDUFAF5, WARS1, RAB3IP, LARGE2, DPAGT1, DUSP16, KDM3B, KMT2B, NQO2, COA1, GARS1-DT, TPP2, NMRK1, MMEL1, ABCA11P, UPP1, PHF1, TMEM218, MAP7D3, ZNF653, AC010175.1, DHODH, TUBGCP6, TUBGCP6, TTLL3, TEX10, SPATS2, ZNF76, FKRP, SAR1B, ZEB2, COA1, SLC44A2, BCLAF3, TRMT2B, PITPNM2, IFT52, P4HA1, NUTM2A-AS1, SIGIRR, ACAD10, ZMYM5, AC243960.1, ZMYM3, VNN2, SERINC5, POGLUT3, LAIR1, BAZ2A, FCGRT, GGA1, TMEM161B-AS1, KRIT1, SAMD4B, FRG1CP, ACADVL, KIF27, NBPF12, NUP62, CEP295, RHNO1, FANCI, RMDN1, UBA52, ELF4, MVK, WASHC2A, TMEM79, BANP, EBLN3P, ITGB3BP, TMEM267, SLC25A37, SERPING1, AC087632.2, TGFB3, TPT1-AS1, LGMN, INO80C, INO80C, TAF11, ATRIP, NCOR2, GTDC1, CPVL, PVT1, RNPS1, A1BG-AS1, PCBP1-AS1, CAMLG, TMBIM1, SLC15A2, DENND4C, MAP3K20, RAB4A, NOD2, ERMARD, ZNF354B, NOTCH2, IP6K2, HLTF, TRAF3IP2-AS1, CCNL1, SYTL2, DGUOK, AGPAT5, VNN2, R3HCC1L, KIF27, LINC00963, JAK3, PPP4R1L, HM13, HM13, GMFG, GGA1, CCM2, LY96, EIF4G3, SNX25, METTL15, CEP290, MAP4, DPEP2, TCEA3, ST6GALNAC4, CASP5, DLGAP4, RBIS, LUCAT1, PSTK, GLT1D1, GTF2I, NRDE2, ST3GAL2, SNAP23, AC138894.1, LMAN2L, CERS4, PGAP2, SLC12A2, CAMK4, ABRAXAS1, FCRL2, TANGO2, GGCT, AP001781.2, NOD2, FYN, CYBC1, CCDC191, ABHD12, FOPNL, NEXN, HFE, TRMT2B, ABCD4, AC243960.1, PSMG4, IKBKG, TRMT61B, IGHG3, ING3, RPL32P3, ABHD14A-ACY1, TBCD, RPAIN, SULT1A1, TCFL5, TCF25, COX20, SERGEF, KIAA2026, CD40, KIR2DL1, GPR141, LRRC37B, TMEM44-AS1, TYSND1, FGR, ZNF133, BCL2L13, PMS2, ARHGAP19, TRIM34, ZBTB8OS, RESF1, CHD4, ZNF133, RBM23, PCBP1-AS1, TMEM116, PI4KB, SNRPA1, PCBP1-AS1, HMOX2, GMDS-DT, IL18R1, UPB1, ZNF138, GATC, PIK3C2B, UPF3A, ANGEL2, KRIT1, CHD4, SRPK2, EVA1C, ACCS, DDX60L, RBIS, N4BP2L2, PCBP1-AS1, ERICH6-AS1, ATP5MC2, SRP54-AS1, ZBTB1, DTNBP1, FAM228B, METTL6, KPTN, POLK, PGS1, RPRD1B, LINC00426, CD160, TAF2, IL15RA, ANXA11, RALGAPB, FAM13B, KIAA1191, DPEP2, CD226, PTPRA, ZNF75D, NABP1, EME2, SNRNP70, TRPV2, PLBD1-AS1, UBE3B, CEP68, ABRAXAS1, NLRP6, RIDA, UBE3B, AC243960.1, DPY19L1, CLEC4C, MADD, CBWD3, ANP32A, ENDOV, FCGRT, RNF8, TFB1M, LONP2, TMEM161B-AS1, TMEM161B-AS1, POLK, PCBP1-AS1, RAB3A, SLC37A3, MIR762HG, MRS2, TXNDC11, LUCAT1, CERS5, INO80E, LUCAT1, AC096887.1, IRAK3, SGCB, CEP41, MPC1, PPP2R2D, TOGARAM2, SLC25A37, ERLIN1, COQ5, TAF1C, SNRNP70, INTS7, DSTYK, CD44, RPL5, CCDC138, RMND5B, SLC66A2, MAK, ABITRAM, AC000120.4, TAMM41, SP140, STAMBP, UBXN8, CHROMR, FANCG, FGR, DPEP2, RALGAPB, C1orf162, GOLGA2P5, GMFG, AC147651.1, IQCB1, ERLIN1, ATOX1, RIDA, TSPAN5, SNHG17, MVK, PSME3IP1, POLK, WDR20, DDX31, POLD1, CAST, TM7SF2, NSRP1, FAM210A, MYL5, INO80C, SIMC1, ABHD16A, DAP3, ANKRD26, ADCY10P1, ADAP2, RPL5, ZCWPW1, SUSD3, CHROMR, TMEM126A, ZFP1, ZNF195, FPR2, DCLRE1C, POU6F1, RPF2, MTSS1, TOP1MT, CPVL, PTPA, PANK2, RGS18, CKLF, PAK1, HM13, LINC01934, BBOF1, BMPR2, AF117829.1, THTPA, C11orf80, UBL7, TRIM5, DICER1-AS1, AC009022.1, POLR2J3, MATR3, CBWD3, POU6F1, TYSND1, BBOF1, NBR2, CCM2, MAP3K8, AC008035.1, LDLRAD4, PSMG4, ANAPC10, ZMYM1, ADCY10P1, TCFL5, POLL, DPH7, MOK, MECP2, HLA-DPA1, HM13, MVK, ZBTB8OS, DOCK2, WBP1, VMP1, MYOM1, FYB1, EVA1C, AC093157.1, TRAF3IP1, SNHG17, YWHAH, ARMCX5-GPRASP2, AC009022.1, ZNF232, CENPN, WBP1, ITGB3BP, MPV17, MTIF3, LRRC23, TMEM143, NEIL2, TMEM161B-AS1, INTS7, TRAF3IP2-AS1, GOLGA8A, BBS9, PPIEL, TUBGCP4, AC060780.1, ECHDC2, UROS, MAFG, GIPR, HCLS1, AC016727.1, SNHG17, AC022137.3, CWF19L1, LRRC23, TMEM143, VNN2, AAMDC, TPRKB, FCHSD1, PYROXD2, STRA6LP, SERPINB9P1, AC245100.4, PGAP3, and combinations thereof.
68. The method of any one of Embodiments 1-56, wherein the mutually exclusive exon is selected from the group consisting of CR1, PIGL, XPNPEP3, MAPKBP1, TBC1D12, AC004593.2, AC016831.6, WDR60, ZNF720, MYO15B, HSD17B3, WHAMMP3, AL392172.1, ATXN2, AL356481.1, PDE8A, ZNF266, AL162258.1, CAMKK1, PPFIA1, ZNF266, CFAP70, ACCS, ATF7IP2, NEIL2, TAF4, PNPT1, HLA-DRB5, DDX60L, YAF2, SP140, KIAA1841, TNNT3, ARFIP1, TUBD1, POMZP3, SH3TC1, POLR2J4, CDKL3, CD300LF, ELP1, RPTOR, ZNF266, POLR2J4, CBWD3, WDR12, PVT1, LLGL2, TCFL5, MCTP1, ST3GAL5, UBXN8, ATXN2, MICA, CARD8, CARD8, AL121845.3, IL32, GMPPB, ZEB2, TBC1D8, LEMD3, SLC38A1, JARID2, SLC38A9, AC119396.1, UBE3C, MARCHF8, TUBGCP4, SLAMF1, GTF2H2, IRF8, POMZP3, MCM6, PVT1, NIBAN3, NFS1, KDM3B, AC114490.2, ZC3H13, TGS1, CR1, POMZP3, POMZP3, DDX21, SYNE1, ZBTB17, MYOM1, TIMM23B-AGAP6, SBNO1, RAB11FIP3, CNOT1, NMRK1, IRF8, TSC2, RCHY1, PVT1, COG8, FKBP15, PLBD1-AS1, TOM1, SUGP1, MCTP1, ZNF185, TAF1D, CELF1, PIGG, C11orf80, ZNF638, TRIM14, NEIL2, SNX9, NSUN6, MRTFA, SLC3A2, SNAPC1, ING4, SERF2, FAM114A2, CELF1, NFKB2, VARS1, CLEC17A, TMEM184B, EML2, CCM2, WRNIP1, DENND4B, AL392172.1, TMEM131, RYK, TMCO3, FOXP1, DNMT1, ZNF254, TCFL5, PILRB, IDH1, NUP98, DDB2, IGHD, POLR2J3, UBAP2L, TSEN2, COA1, MPHOSPH6, CERS4, AC069281.2, ATP2B4, EIF4G1, WDFY3, ECPAS, SLC25A19, STAU2, RPS6KA3, DUS2, MAN1B1, KMT2D, RRP8, SPAG9, CPNE1, UBXN11, SLC44A2, KDM5A, TNPO1, HEATR5B, RNF170, RHOT1, TMEM50B, SCLT1, MAN2B1, PCBP1-AS1, AC069281.2, DTNBP1, PINK1, HDAC7, CMTM1, CDC23, PCBP1-AS1, PCBP1-AS1, EHBP1L1, ANKZF1, AC118553.2, NAE1, GIT1, CREBBP, RALY, XAF1, CCM2, CPSF7, CAST, SMG5, PVT1, RGS6, SUMF2, RALY, RALY, MLKL, ITPA, GATAD2A, MKNK1, MIR4435-2HG, SSBP4, CCM2, TNFRSF1A, TLE3, ARHGAP25, TRAK1, LRCH3, TLE3, PLD3, ADA, SHISA5, NCF1, NUP88, USB1, FMNL1, CYB5R4, NFKB2, NUP88, RCBTB2, STRADA, CRTC2, UNC13D, ICE1, TMBIM1, SH2D3C, SLC44A2, SORL1, LTBR, CHP1, CTDNEP1, RPS12, WDFY4, FANCA, CPNE1, CPNE1, OSBPL11, RHOT1, ITGAL, INTS8, DBNL, GSN, CNOT3, DAGLB, DBNL, STXBP2, SNHG29, UNC13D, FCHO1, SLC35C2, WDR47, MKNK2, INPP5D, LRCH4, TTC7A, UNC93B1, PDE4B, HLA-DRB1, TNFRSF1A, AC118553.2, FGR, COG4, FLOT1, CAMK1D, LMBR1, TSC2, FGR, NAA60, INTS6, TTC16, H2AZ2, AC004997.1, SPTLC1, BAG6, TTC17, CDK16, NAXD, IGFLR1, GOLGA7, YY1AP1, YY1AP1, CASC4, PTDSS1, CEP290, TIMM23B-AGAP6, IL21R, DNMT1, PDIA4, SIPA1, POLR2F, POLL, PSMA5, PAFAH2, MOV10, HMGB2, PYCR2, B4GALT3, RHOT2, DDX17, NQO2, WDR70, INTS8, EXOSC1, RABEPK, UTP6, TRPC4AP, XAF1, ZDHHC4, PHYKPL, CAST PPA2, RBM6, DDX21, RCBTB2, ABCA7, LMF2, PHC2, WDSUB1, JAK1, IFTAP, RABEPK, SNX10, DAGLB, DEK, WDSUB1, LAIR1, VDAC2, PPP4R3B, DLEU2, STK38, STAT5B, DES11, CCM2, PREX1, TMEM87A, NEPRO, WDR37, LAIR1, LAIR1, SUPT20H, CDC16, JPX, RBM23, RPL18A, LINC00893, ZDHHC4, SND1, SLC3A2, RBM33, TMEM63A, MEF2D, NLRC5, POLD2, TNFSF13, NTAN1, VPS53, TANGO2, ARHGEF40, ZDHHC24, ABCA7, SAMD9L, EPSTI1, POLR3C, ECHDC1, GMDS-DT, WDSUB1, TYROBP, TTC13, PHF20L1, CORO1C, ECHDC1, SMIM8, NEPRO, HLA-C, BBS9, AMD1, ERCC1, DLG1, ZFAND1, MAPKAPK5, CELF1, PVT1, WASH3P, CNOT2, RFFL, LONP2, ARIH2, SNX22, SCAP, VASP, FKBP15, PSD4, INTS8, TANGO2, TMEM127, LRCH3, KDM5C, BBS1, SRP14-AS1, SOS1, RNF121, PDCD6, SEC16A, ADAP2, DNAJC2, RPS6 KB1, RNF121, CEP290, PVT1, EXOSC9, CLPTM1, PREX1, IL15, MTA1, EFCAB13, OCEL1, ZC3H7A, DAGLB, EIF2B4, EIF2D, GUSBP11, FBXO3, VASP, GRK3, PIK3AP1, CDC16, RALGAPB, PAPSS1, RABGAP1L, C1orf21, LAIR1, ST6GAL1, OGFOD1, ARAP2, FDX1, TTC39B, CD320, RUNX3, COP1, ANKRD27, TXLNA, TPGS2, MCTP1, AD000671.1, COQ7, NRF1, IFTAP, SCFD1, LY96, TMCO4, ANKZF1, SCYL1, PTPRA, DRAM1, USP48, ARHGEF40, CHFR, GYS1, RORC, UVRAG, SIRPB1, TTI2, COP1, TMEM8B, CAPN12, HIPK3, SRC, HERPUD2, KLRG1, COP1, WDSUB1, SPG7, P4HA1, IKBKG, METTL26, DNAJC1, NACC2, THOC6, ALG13, RB1, LRP8, BCAS3, RNF170, MDM4, METTL26, FANCA, CWF19L1, LRRK2, PRMT9, NUP54, ANKZF1, NAE1, PPP2R2D, TSEN2, IKBKG, THEM4, COP1, CAST, AGPAT3, TRPM7, RAD1, RNPC3, WDSUB1, SLBP, KIF1C, FOXRED1, DICER1-AS1, CRBN, PACC1, SPATA13, ABCB7, DENND4B, JAK2, N4BP2L1, IMMP1L, TBC1D2B, ATF7IP, SLBP, ARHGAP19, POLL, IL15, RIN3, PXN, PLXDC1, N4BP2L1, PI4KAP2, SUZ12P1, SCAF8, GTF2IRD2B, SENP6, DNMT3A, DCP1B, TMEM39A, CBWD3, RETSAT, DENND6A, ZSWIM7, AK5, MDM1, ITGA6, HDAC4, SIRPB1, ELMO2, ABCA7, HLA-B, KIAA0753, MRNIP, RIOK1, HLA-B, RNF144B, RAB35, DOCK10, FBXL4, TMEM189-UBE2V1, SEPTIN11, RBM22, BSCL2, SNHG17, SORBS3, SPOPL, SLC7A6, NDRG1, LAIR1, LAIR1, ATL2, SCAF8, AC009061.2, TMCO4, BSCL2, MAPK6, PLSCR3, FOXJ3, SLC39A11, PYROXD1, RNF144B, TMEM220, TADA2A, CYRIB, PEX1, TSPAN2, TTLL12, TMEM234, BCL9L, AC0008073.3, GNB4, TSPAN2, TMEM234, ERAP2, ANKRD6, DDX60L, GTF2H2B, SLC35F2, TBCD, ZFR, PXYLP1, SOS1, SNHG17, CA5B, SNHG17, ERC1, CYRIB, RANBP10, AC092070.2, SETD6, ITGB2, CEP170, SNHG17, LRP8, SNHG17, ANKRD36B, and combinations thereof.
69. The method of any one of Embodiments 1-56, wherein the alternative 3′ splicing site is selected from the group consisting of PATZ1, TPTEP1, PABPC1L, SNHG17, CPNE1, CPNE1, ZNF160, XAF1, LSM7, POLR2J3, TSNARE1, THADA, TRIM73, AEBP1, TBC1D7, DDX60L, ASNS, MTSS1, MZB1, SEPTIN8, PPWD1, TMEM116, TMEM116, BRD9, SDHA, IKBKG, ZNF707, CEP131, DXO, TAFA2, TPRG1, DLG1, GGT1, SRGAP2, TMEM161B-AS1, HLA-C, CCDC163, NABP1, RNF181, CENPT, KHDC4, ZNF7, DCAF11, AK5, ARRB2, ARHGAP25, AHSA2P, AZIN1, ZNF540, MFSD9, JKAMP, HARS2, RNF32, BPHL, PPP6R3, PPP6R3, HELB, GALT, ALAD, LAIR1, LAIR1, AC016394.2, CTSB, NAPIL4, ZNF195, TCTN1, PHB2, PHF1, ATG16L2, TMEM25, SPSB2, YAF2, MAP3K12, ATXN2, ARL6IP4, TMEM273, MPP5, ALDH6A1, LTK, FAM219B, MAN2A2, PSTPIP1, ZNF23, SPG7, GABBR1, MLX, BRCA1, TSPOAP1-AS1, DPH2, MPPE1, CCDC191, PCBP1-AS1, PCBP1-AS1, PCBP1-AS1, VPS33B, UNC50, ZNF345, and combinations thereof.
70. The method of any one of Embodiments 1-56, wherein the alternative 5′ splicing site is selected from the group consisting of PQBP1, PIGT, TTPAL, FNTA, NEIL2, CEP152, DEPDC5, HLA-DMA, MICA, MSTO1, MSTO1, MSTO1, ERAP2, PARP2, ZSCAN25, HAGHL, BUD31, FCRL1, AL392172.1, NDUFV2, ERVK13-1, ERVK13-1, APTR, KLRD1, IRF3, CUL7, ZDHHC3, ZDHHC3, RBIS, PCBP4, ATP5F1A, LUCAT1, CCDC14, UBE2I, ELOA-AS1, SLC25A37, AGA, CNBP, PPIEL, AC022400.7, MRPL43, MRPL43, SERGEF, STAT2, ULK3, SLC6A12, ANXA2, ITGB7, TM6SF1, ARL6IP4, DDX51, UBAC2-AS1, PXN-AS1, APEX1, NEK3, NEK3, TPM1, SMPD1, UBC, DVL2, DPH2, AC243960.1, and combinations thereof.
71. The method of any one Embodiments 1-56, wherein the gene is selected from the group consisting of GPATCH4, CAPN3, SUN1, ZNF7, ATAT1, PER1, MSTO1, DHRS4L2, RELA-DT, TM7SF2, DERL3, ASB16-AS1, FAN1, ZFC3H1, NRBP2, OGFOD2, SUN1, AAAS, LILRA1, BPHL, DDX51, ZNF266, WDR54, BCS1L, FCSK, SEC31B, POLG, CD3E, CD19, TUBGCP4, AVIL, ZNF160, MINK1, TTC16, ING4, FCGR2B, GINS4, C1R, TRIM27, RABEPK, CTC1, MAN2C1, RASGRP4, WDR24, RINL, ZSCAN25, OGFOD2, C1orf174, PAXX LINC01128, PRICKLE3, IRF3, MUTYH, FAHD2A, RIOK1, ZC3H14, TMEM208, HARS2, MAP4K2, WDR6, ZNF649, NEPRO, BEST1, THOC6, PFKM, ADA, IFT43, PPIE, BTN3A3, SAMD9L, MPPE1, IFFO1, NAGK, CCDC159, SAP30BP, MRNIP, ARHGAP9, XPOT, P3H1, REC8, SCML4, APEX1, ENDOV, HMBS, BRPF1, DHRS1, NPHP3, KLF4, CALCOCO1, RPAIN, CIRBP, KRIT1, BSDCI, GALT, TMEM150A, ZSWIM8, DPH1, TMEM205, CARD8, LFNG, NDUFAF7, ARGLU1, RNF44, NRBP2, ERVK13-1, ZNF7, MSTO1, MIB2, TMEM147, BBS1, ZNF160, ZNF577, MFSD2A, VPS11, PPOX, CDK16, MIB2, PRPF40B, STARD5, MIB2, CDK16, ALG9, PPIEL, HTRA2, MAN2C1, ZNF528-AS1, MYO1G, PHYHD1, SNHG17, TCL6, NMRK1, and combinations thereof.
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The teachings of all patents, published applications and references cited herein are incorporated by reference in their entirety.
While example embodiments have been particularly shown and described, it will be understood by those skilled in the art that various changes in form and details may be made therein without departing from the scope of the embodiments encompassed by the appended claims.
